Starting phenix.real_space_refine on Wed Mar 12 08:01:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2z_43760/03_2025/8w2z_43760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2z_43760/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2z_43760/03_2025/8w2z_43760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2z_43760/03_2025/8w2z_43760.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2z_43760/03_2025/8w2z_43760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2z_43760/03_2025/8w2z_43760.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'HIS:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} 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: 5.70, per 1000 atoms: 0.74 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: 2.11 Conformation dependent library (CDL) restraints added in 494.1 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: 3.36 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: 3.30 Time building geometry restraints manager: 2.49 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: 2.570 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- 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= 0.281 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.006 TRP A 452 HIS 0.012 0.002 HIS A 145 PHE 0.048 0.003 PHE A 599 TYR 0.012 0.002 TYR A 169 ARG 0.019 0.002 ARG A 152 *********************** 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 : 0.580 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: 0.2572 time to fit residues: 19.3101 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 : 0.562 ------------------------------------------------------------------------------- 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 56 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.136646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095107 restraints weight = 14596.829| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.07 r_work: 0.3062 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8156 Z= 0.425 Angle : 0.740 10.666 11795 Z= 0.398 Chirality : 0.048 0.859 1441 Planarity : 0.005 0.037 882 Dihedral : 22.782 167.129 3043 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.12 % Allowed : 15.98 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.36), residues: 513 helix: 0.27 (0.37), residues: 181 sheet: -1.35 (0.59), residues: 65 loop : -1.61 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 452 HIS 0.009 0.002 HIS A 244 PHE 0.025 0.002 PHE A 648 TYR 0.014 0.002 TYR A 169 ARG 0.011 0.001 ARG A 568 *********************** 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 78 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7429 (tmm-80) cc_final: 0.7158 (tmm-80) REVERT: A 185 GLU cc_start: 0.3757 (OUTLIER) cc_final: 0.3435 (tm-30) REVERT: A 591 LYS cc_start: 0.7597 (tttt) cc_final: 0.6691 (pptt) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 0.2868 time to fit residues: 27.0193 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 : 0.579 ------------------------------------------------------------------------------- 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 696 LEU 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 12 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.140516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097281 restraints weight = 15021.048| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.18 r_work: 0.3100 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1635 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= 0.172 Angle : 0.570 9.205 11795 Z= 0.315 Chirality : 0.040 0.694 1441 Planarity : 0.004 0.030 882 Dihedral : 22.689 170.707 3043 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.91 % Allowed : 18.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.38), residues: 513 helix: 1.06 (0.40), residues: 179 sheet: -0.83 (0.65), residues: 56 loop : -1.43 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 452 HIS 0.005 0.001 HIS A 244 PHE 0.012 0.001 PHE A 648 TYR 0.007 0.001 TYR A 169 ARG 0.012 0.001 ARG A 456 *********************** 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 70 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.623 Fit side-chains REVERT: A 185 GLU cc_start: 0.3520 (OUTLIER) cc_final: 0.3194 (tm-30) REVERT: A 456 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8407 (tmm-80) REVERT: A 591 LYS cc_start: 0.7795 (tttt) cc_final: 0.6589 (pptt) REVERT: A 735 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8331 (m) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.2820 time to fit residues: 24.1807 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.139878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096537 restraints weight = 14940.142| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1897 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= 0.196 Angle : 0.567 9.468 11795 Z= 0.314 Chirality : 0.040 0.708 1441 Planarity : 0.004 0.029 882 Dihedral : 22.622 168.545 3043 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.63 % Allowed : 17.68 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.38), residues: 513 helix: 1.28 (0.40), residues: 181 sheet: -0.64 (0.64), residues: 56 loop : -1.50 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 PHE 0.013 0.001 PHE A 648 TYR 0.007 0.001 TYR A 169 ARG 0.006 0.001 ARG A 456 *********************** 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 69 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.735 Fit side-chains REVERT: A 185 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.3183 (tm-30) REVERT: A 574 GLU cc_start: 0.6858 (tp30) cc_final: 0.6543 (tp30) REVERT: A 580 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5819 (mp0) REVERT: A 591 LYS cc_start: 0.7938 (tttt) cc_final: 0.6511 (tmmt) REVERT: A 735 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8596 (m) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.2606 time to fit residues: 22.1207 Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 580 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 587 THR 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 63 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.136237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092550 restraints weight = 14917.997| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.26 r_work: 0.3011 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2323 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= 0.328 Angle : 0.661 12.125 11795 Z= 0.357 Chirality : 0.045 0.853 1441 Planarity : 0.004 0.037 882 Dihedral : 22.690 166.941 3043 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.15 % Allowed : 18.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.38), residues: 513 helix: 1.17 (0.40), residues: 181 sheet: -0.67 (0.61), residues: 58 loop : -1.67 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 452 HIS 0.005 0.001 HIS A 239 PHE 0.019 0.001 PHE A 648 TYR 0.010 0.002 TYR A 169 ARG 0.005 0.001 ARG A 460 *********************** 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 69 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8395 (m-80) cc_final: 0.7959 (m-80) REVERT: A 185 GLU cc_start: 0.3594 (OUTLIER) cc_final: 0.2503 (tm-30) REVERT: A 699 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8173 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.2343 time to fit residues: 20.5107 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 : 0.651 ------------------------------------------------------------------------------- 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 587 THR 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 58 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 = 0.138065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094802 restraints weight = 14849.913| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.24 r_work: 0.3049 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8156 Z= 0.226 Angle : 0.598 9.670 11795 Z= 0.326 Chirality : 0.041 0.761 1441 Planarity : 0.004 0.071 882 Dihedral : 22.653 166.151 3043 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.63 % Allowed : 18.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.37), residues: 513 helix: 1.26 (0.40), residues: 181 sheet: -0.75 (0.57), residues: 61 loop : -1.69 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 452 HIS 0.004 0.001 HIS A 239 PHE 0.013 0.001 PHE A 648 TYR 0.007 0.001 TYR A 169 ARG 0.008 0.001 ARG A 460 *********************** 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 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8359 (m-80) cc_final: 0.7951 (m-80) REVERT: A 185 GLU cc_start: 0.3482 (OUTLIER) cc_final: 0.2394 (tm-30) outliers start: 15 outliers final: 12 residues processed: 68 average time/residue: 0.2426 time to fit residues: 21.4817 Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 587 THR 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 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 0.0050 chunk 51 optimal weight: 9.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096808 restraints weight = 14925.388| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.02 r_work: 0.3092 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2666 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= 0.180 Angle : 0.568 9.109 11795 Z= 0.311 Chirality : 0.039 0.692 1441 Planarity : 0.005 0.111 882 Dihedral : 22.584 164.594 3043 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.37), residues: 513 helix: 1.41 (0.40), residues: 181 sheet: -0.23 (0.61), residues: 54 loop : -1.60 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 PHE 0.010 0.001 PHE A 648 TYR 0.008 0.001 TYR A 454 ARG 0.006 0.000 ARG A 460 *********************** 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 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8369 (m-80) cc_final: 0.7965 (m-80) REVERT: A 185 GLU cc_start: 0.3534 (OUTLIER) cc_final: 0.2434 (tm-30) REVERT: A 203 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8390 (tm-30) outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.2211 time to fit residues: 18.3006 Evaluate side-chains 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 299 ILE 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 60 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.137246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094187 restraints weight = 15039.255| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.12 r_work: 0.3038 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8156 Z= 0.252 Angle : 0.595 9.737 11795 Z= 0.325 Chirality : 0.042 0.774 1441 Planarity : 0.005 0.092 882 Dihedral : 22.617 164.996 3043 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.91 % Allowed : 19.37 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.37), residues: 513 helix: 1.36 (0.40), residues: 181 sheet: -0.55 (0.56), residues: 61 loop : -1.60 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 PHE 0.014 0.001 PHE A 648 TYR 0.008 0.001 TYR A 95 ARG 0.009 0.001 ARG A 460 *********************** 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 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3667 (OUTLIER) cc_final: 0.2628 (tm-30) REVERT: A 203 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8398 (tm-30) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.2326 time to fit residues: 17.6441 Evaluate side-chains 57 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 450 ILE 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 40 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091135 restraints weight = 15094.469| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.35 r_work: 0.2980 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8156 Z= 0.342 Angle : 0.666 10.535 11795 Z= 0.361 Chirality : 0.046 0.899 1441 Planarity : 0.005 0.059 882 Dihedral : 22.715 166.415 3043 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.91 % Allowed : 20.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.37), residues: 513 helix: 1.19 (0.40), residues: 179 sheet: -0.52 (0.58), residues: 61 loop : -1.66 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 452 HIS 0.004 0.001 HIS A 239 PHE 0.019 0.002 PHE A 648 TYR 0.013 0.002 TYR A 95 ARG 0.010 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3975 (OUTLIER) cc_final: 0.3065 (tm-30) REVERT: A 203 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8363 (tm-30) REVERT: A 582 ASP cc_start: 0.8175 (t0) cc_final: 0.7958 (t0) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.2559 time to fit residues: 19.6959 Evaluate side-chains 61 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 299 ILE 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 49 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 10 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.7288 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.138737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095929 restraints weight = 15036.651| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.16 r_work: 0.3069 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3089 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= 0.166 Angle : 0.559 8.784 11795 Z= 0.305 Chirality : 0.039 0.682 1441 Planarity : 0.004 0.047 882 Dihedral : 22.570 165.795 3043 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.37), residues: 513 helix: 1.43 (0.40), residues: 181 sheet: 0.04 (0.61), residues: 53 loop : -1.60 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 452 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE A 570 TYR 0.007 0.001 TYR A 76 ARG 0.010 0.001 ARG A 460 ********************** 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: 9 poor density : 51 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 582 ASP cc_start: 0.7944 (t0) cc_final: 0.7638 (t0) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2575 time to fit residues: 19.6743 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 : 0.635 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095455 restraints weight = 14976.427| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.16 r_work: 0.3065 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3162 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= 0.190 Angle : 0.568 9.116 11795 Z= 0.309 Chirality : 0.040 0.708 1441 Planarity : 0.004 0.041 882 Dihedral : 22.542 165.388 3043 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.18 % Allowed : 21.55 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 513 helix: 1.49 (0.39), residues: 181 sheet: -0.01 (0.61), residues: 54 loop : -1.54 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 452 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE A 235 TYR 0.007 0.001 TYR A 76 ARG 0.009 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.80 seconds wall clock time: 67 minutes 30.42 seconds (4050.42 seconds total)