Starting phenix.real_space_refine on Wed Feb 12 07:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2z_43760/02_2025/8w2z_43760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2z_43760/02_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_43760/02_2025/8w2z_43760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2z_43760/02_2025/8w2z_43760.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2z_43760/02_2025/8w2z_43760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2z_43760/02_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-5592/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: 5.36, per 1000 atoms: 0.70 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: 2.27 Conformation dependent library (CDL) restraints added in 527.0 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: 3.30 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: 3.79 Time building geometry restraints manager: 2.55 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: 1.380 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- 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 : 0.556 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: 0.2511 time to fit residues: 18.8561 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 : 0.546 ------------------------------------------------------------------------------- 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 = 0.136617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094900 restraints weight = 14610.269| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.08 r_work: 0.3051 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1630 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 10.664 11795 Z= 0.399 Chirality : 0.048 0.859 1441 Planarity : 0.005 0.037 882 Dihedral : 22.782 167.122 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: 0.26 (0.37), residues: 181 sheet: -1.34 (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 0.008 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 : 0.598 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7375 (tmm-80) cc_final: 0.7111 (tmm-80) REVERT: A 185 GLU cc_start: 0.3815 (OUTLIER) cc_final: 0.3497 (tm-30) REVERT: A 591 LYS cc_start: 0.7577 (tttt) cc_final: 0.6703 (pptt) outliers start: 17 outliers final: 8 residues processed: 74 average time/residue: 0.2683 time to fit residues: 25.4502 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098258 restraints weight = 14944.734| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3122 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1615 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= 0.164 Angle : 0.572 9.158 11795 Z= 0.314 Chirality : 0.039 0.684 1441 Planarity : 0.004 0.031 882 Dihedral : 22.689 171.101 3043 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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 (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: -0.67 (0.38), residues: 513 helix: 1.04 (0.40), residues: 179 sheet: -0.81 (0.65), residues: 56 loop : -1.41 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 452 HIS 0.005 0.001 HIS A 244 PHE 0.012 0.001 PHE A 648 TYR 0.006 0.001 TYR A 169 ARG 0.011 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 68 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.610 Fit side-chains REVERT: A 185 GLU cc_start: 0.3435 (OUTLIER) cc_final: 0.3117 (tm-30) REVERT: A 456 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8368 (tmm-80) REVERT: A 591 LYS cc_start: 0.7788 (tttt) cc_final: 0.6578 (pptt) REVERT: A 735 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8289 (m) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.2948 time to fit residues: 24.5181 Evaluate side-chains 56 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.141069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099976 restraints weight = 14924.285| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.99 r_work: 0.3118 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1836 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= 0.177 Angle : 0.557 9.281 11795 Z= 0.308 Chirality : 0.039 0.685 1441 Planarity : 0.004 0.028 882 Dihedral : 22.615 169.071 3043 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.15 % Allowed : 18.16 % 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: -0.53 (0.38), residues: 513 helix: 1.29 (0.40), residues: 181 sheet: -0.67 (0.64), residues: 56 loop : -1.46 (0.39), 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 0.012 0.001 PHE A 648 TYR 0.006 0.001 TYR A 169 ARG 0.004 0.001 ARG A 229 *********************** 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 67 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.504 Fit side-chains REVERT: A 185 GLU cc_start: 0.3586 (OUTLIER) cc_final: 0.3234 (tm-30) REVERT: A 580 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5818 (mp0) REVERT: A 591 LYS cc_start: 0.7895 (tttt) cc_final: 0.6423 (tmmt) REVERT: A 598 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8169 (mtm-85) REVERT: A 610 LYS cc_start: 0.7664 (tptp) cc_final: 0.7457 (tptp) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.2669 time to fit residues: 21.8430 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 : 0.546 ------------------------------------------------------------------------------- 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 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 63 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090242 restraints weight = 14858.576| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.22 r_work: 0.3063 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2276 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= 0.302 Angle : 0.646 13.828 11795 Z= 0.349 Chirality : 0.044 0.830 1441 Planarity : 0.004 0.031 882 Dihedral : 22.677 167.217 3043 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.39 % Allowed : 18.16 % 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 (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: -0.66 (0.38), residues: 513 helix: 1.23 (0.40), residues: 181 sheet: -0.64 (0.60), residues: 58 loop : -1.62 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 452 HIS 0.004 0.001 HIS A 239 PHE 0.019 0.002 PHE A 648 TYR 0.009 0.001 TYR A 169 ARG 0.004 0.001 ARG A 37 *********************** 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 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8383 (m-80) cc_final: 0.7961 (m-80) REVERT: A 185 GLU cc_start: 0.3465 (OUTLIER) cc_final: 0.2445 (tm-30) REVERT: A 574 GLU cc_start: 0.7082 (tp30) cc_final: 0.6623 (tp30) REVERT: A 588 TYR cc_start: 0.7608 (m-80) cc_final: 0.7399 (m-80) REVERT: A 699 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8196 (mtm-85) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.2484 time to fit residues: 22.0757 Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 623 GLU 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: 0.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.9462 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.139359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095985 restraints weight = 14860.044| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.14 r_work: 0.3082 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2405 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= 0.180 Angle : 0.581 12.471 11795 Z= 0.315 Chirality : 0.040 0.707 1441 Planarity : 0.004 0.059 882 Dihedral : 22.610 167.512 3043 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 (0.38), residues: 513 helix: 1.36 (0.40), residues: 182 sheet: -0.70 (0.57), residues: 61 loop : -1.56 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 452 HIS 0.002 0.001 HIS A 653 PHE 0.012 0.001 PHE A 648 TYR 0.007 0.001 TYR A 169 ARG 0.010 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 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8337 (m-80) cc_final: 0.7967 (m-80) REVERT: A 185 GLU cc_start: 0.3468 (OUTLIER) cc_final: 0.2379 (tm-30) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.2397 time to fit residues: 19.4955 Evaluate side-chains 59 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.135875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092154 restraints weight = 14844.252| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.31 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: 0.8462 moved from start: 0.2727 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= 0.326 Angle : 0.659 11.435 11795 Z= 0.356 Chirality : 0.045 0.861 1441 Planarity : 0.006 0.141 882 Dihedral : 22.669 165.400 3043 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -0.63 (0.38), residues: 513 helix: 1.26 (0.40), residues: 180 sheet: -0.55 (0.57), residues: 61 loop : -1.62 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 452 HIS 0.003 0.001 HIS A 653 PHE 0.019 0.002 PHE A 648 TYR 0.011 0.002 TYR A 95 ARG 0.005 0.001 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 67 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3714 (OUTLIER) cc_final: 0.2638 (tm-30) REVERT: A 203 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 460 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.8185 (mtp85) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.2499 time to fit residues: 21.0907 Evaluate side-chains 59 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.136104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092873 restraints weight = 14977.085| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.20 r_work: 0.3014 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2848 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= 0.289 Angle : 0.629 9.960 11795 Z= 0.340 Chirality : 0.044 0.812 1441 Planarity : 0.006 0.115 882 Dihedral : 22.685 165.692 3043 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.66 % Allowed : 19.85 % 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 (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: -0.63 (0.37), residues: 513 helix: 1.23 (0.40), residues: 181 sheet: -0.49 (0.56), residues: 61 loop : -1.62 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 452 HIS 0.003 0.001 HIS A 653 PHE 0.015 0.001 PHE A 648 TYR 0.009 0.002 TYR A 670 ARG 0.007 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 65 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3821 (OUTLIER) cc_final: 0.2831 (tm-30) REVERT: A 203 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 460 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8226 (mtp85) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.2360 time to fit residues: 19.6972 Evaluate side-chains 61 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 40 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092161 restraints weight = 15024.135| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.24 r_work: 0.3002 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3003 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= 0.290 Angle : 0.633 9.970 11795 Z= 0.343 Chirality : 0.044 0.831 1441 Planarity : 0.005 0.103 882 Dihedral : 22.662 166.077 3043 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.42 % Allowed : 20.34 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.38), residues: 513 helix: 1.23 (0.40), residues: 180 sheet: -0.48 (0.57), residues: 61 loop : -1.53 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 452 HIS 0.003 0.001 HIS A 653 PHE 0.016 0.001 PHE A 648 TYR 0.010 0.001 TYR A 95 ARG 0.007 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 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3814 (OUTLIER) cc_final: 0.2873 (tm-30) REVERT: A 203 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 460 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7964 (mtp85) REVERT: A 598 ARG cc_start: 0.8715 (ttm170) cc_final: 0.8483 (ttm170) outliers start: 10 outliers final: 9 residues processed: 58 average time/residue: 0.2671 time to fit residues: 19.9164 Evaluate side-chains 59 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- 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 = 0.137223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094049 restraints weight = 15025.293| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.25 r_work: 0.3029 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3061 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= 0.221 Angle : 0.595 9.472 11795 Z= 0.324 Chirality : 0.041 0.762 1441 Planarity : 0.005 0.084 882 Dihedral : 22.615 165.991 3043 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.42 % Allowed : 20.34 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.38), residues: 513 helix: 1.32 (0.40), residues: 181 sheet: -0.50 (0.57), residues: 61 loop : -1.50 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 452 HIS 0.002 0.001 HIS A 244 PHE 0.011 0.001 PHE A 648 TYR 0.008 0.001 TYR A 95 ARG 0.008 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 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3728 (OUTLIER) cc_final: 0.2821 (tm-30) REVERT: A 203 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 459 LEU cc_start: 0.8628 (mp) cc_final: 0.8424 (mp) REVERT: A 460 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7698 (mtp85) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.2534 time to fit residues: 20.3858 Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- 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 = 0.138480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095709 restraints weight = 14959.019| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3150 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= 0.181 Angle : 0.568 8.986 11795 Z= 0.309 Chirality : 0.039 0.693 1441 Planarity : 0.004 0.056 882 Dihedral : 22.528 165.400 3043 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.42 % Allowed : 20.34 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.38), residues: 513 helix: 1.54 (0.40), residues: 179 sheet: -0.33 (0.60), residues: 58 loop : -1.35 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 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 0.009 0.001 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3748.47 seconds wall clock time: 67 minutes 19.41 seconds (4039.41 seconds total)