Starting phenix.real_space_refine on Tue Feb 11 06:20:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpv_44791/02_2025/9bpv_44791.cif" } resolution = 3.0 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= 0.003 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2819 2.51 5 N 749 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 4417 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1613 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1570 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 19, 'TRANS': 176} Chain: "C" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1206 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.23, per 1000 atoms: 0.73 Number of scatterers: 4417 At special positions: 0 Unit cell: (76.68, 91.59, 101.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 821 8.00 N 749 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 130 " distance=2.02 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 103 " distance=2.02 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 162 " distance=2.03 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 Links applied NAG-ASN " NAG B 301 " - " ASN B 122 " " NAG B 302 " - " ASN B 9 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 517.8 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 10 sheets defined 26.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.556A pdb=" N THR A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.921A pdb=" N GLN C 8 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 34 removed outlier: 4.061A pdb=" N LEU C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 55 through 79 removed outlier: 4.548A pdb=" N VAL C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 4.363A pdb=" N VAL C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 151 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32 removed outlier: 4.311A pdb=" N VAL A 27 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 39 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET A 29 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 37 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 31 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 5.634A pdb=" N GLN A 63 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 58 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 65 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR A 56 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET A 67 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 54 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 5.634A pdb=" N GLN A 63 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 58 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 65 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR A 56 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET A 67 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 54 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 15 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 115 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 152 191 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1380 1.34 - 1.46: 773 1.46 - 1.58: 2343 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4534 Sorted by residual: bond pdb=" N PHE C 43 " pdb=" CA PHE C 43 " ideal model delta sigma weight residual 1.462 1.494 -0.032 8.50e-03 1.38e+04 1.45e+01 bond pdb=" N VAL A 191 " pdb=" CA VAL A 191 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL C 59 " pdb=" CA VAL C 59 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.85e+00 bond pdb=" N ILE B 118 " pdb=" CA ILE B 118 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.75e+00 ... (remaining 4529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 5594 1.64 - 3.28: 520 3.28 - 4.92: 45 4.92 - 6.56: 3 6.56 - 8.20: 4 Bond angle restraints: 6166 Sorted by residual: angle pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" C LYS B 58 " ideal model delta sigma weight residual 113.97 105.77 8.20 1.28e+00 6.10e-01 4.11e+01 angle pdb=" C GLU B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 122.08 127.61 -5.53 1.47e+00 4.63e-01 1.41e+01 angle pdb=" CA GLY A 193 " pdb=" C GLY A 193 " pdb=" O GLY A 193 " ideal model delta sigma weight residual 121.18 117.99 3.19 8.80e-01 1.29e+00 1.31e+01 angle pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" C LEU B 60 " ideal model delta sigma weight residual 113.19 108.99 4.20 1.19e+00 7.06e-01 1.24e+01 angle pdb=" CA THR B 57 " pdb=" CB THR B 57 " pdb=" OG1 THR B 57 " ideal model delta sigma weight residual 109.60 104.67 4.93 1.50e+00 4.44e-01 1.08e+01 ... (remaining 6161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2437 17.14 - 34.29: 248 34.29 - 51.43: 70 51.43 - 68.58: 33 68.58 - 85.72: 6 Dihedral angle restraints: 2794 sinusoidal: 1189 harmonic: 1605 Sorted by residual: dihedral pdb=" CB CYS B 175 " pdb=" SG CYS B 175 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 57.98 35.02 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 130 " pdb=" CB CYS B 130 " ideal model delta sinusoidal sigma weight residual 93.00 124.92 -31.92 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS C 38 " pdb=" SG CYS C 38 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -117.68 31.68 1 1.00e+01 1.00e-02 1.43e+01 ... (remaining 2791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 654 0.129 - 0.258: 29 0.258 - 0.387: 0 0.387 - 0.516: 0 0.516 - 0.645: 1 Chirality restraints: 684 Sorted by residual: chirality pdb=" CG LEU C 42 " pdb=" CB LEU C 42 " pdb=" CD1 LEU C 42 " pdb=" CD2 LEU C 42 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA ARG A 28 " pdb=" N ARG A 28 " pdb=" C ARG A 28 " pdb=" CB ARG A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE C 96 " pdb=" N ILE C 96 " pdb=" C ILE C 96 " pdb=" CB ILE C 96 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 681 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " 0.234 9.50e-02 1.11e+02 1.05e-01 6.76e+00 pdb=" NE ARG C 39 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 151 " -0.229 9.50e-02 1.11e+02 1.03e-01 6.47e+00 pdb=" NE ARG C 151 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 151 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 151 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 151 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 88 " 0.214 9.50e-02 1.11e+02 9.59e-02 5.63e+00 pdb=" NE ARG A 88 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 88 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 88 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 334 2.74 - 3.28: 4160 3.28 - 3.82: 7244 3.82 - 4.36: 8868 4.36 - 4.90: 15059 Nonbonded interactions: 35665 Sorted by model distance: nonbonded pdb=" OH TYR B 39 " pdb=" O LYS B 68 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 71 " pdb=" NH1 ARG C 147 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG A 130 " pdb=" O GLN B 163 " model vdw 2.249 3.120 nonbonded pdb=" O VAL A 108 " pdb=" OH TYR A 149 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR B 125 " pdb=" OG1 THR B 180 " model vdw 2.293 3.040 ... (remaining 35660 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: 0.990 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.007 0.039 4534 Z= 0.450 Angle : 0.922 8.202 6166 Z= 0.647 Chirality : 0.063 0.645 684 Planarity : 0.009 0.105 790 Dihedral : 16.577 85.720 1722 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.61 % Allowed : 20.33 % Favored : 79.07 % 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: 0.62 (0.37), residues: 534 helix: 1.47 (0.50), residues: 117 sheet: 0.83 (0.39), residues: 181 loop : -0.41 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 91 HIS 0.006 0.001 HIS C 95 PHE 0.006 0.001 PHE C 43 TYR 0.009 0.001 TYR A 59 ARG 0.005 0.001 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.442 Fit side-chains REVERT: A 160 LYS cc_start: 0.8039 (tttt) cc_final: 0.7760 (ttmt) REVERT: A 182 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7729 (mp0) REVERT: B 117 GLU cc_start: 0.6923 (pt0) cc_final: 0.6610 (pt0) REVERT: B 172 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4660 (tt0) REVERT: B 191 LYS cc_start: 0.8053 (pttp) cc_final: 0.7798 (pttp) REVERT: C 64 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7354 (mt-10) outliers start: 3 outliers final: 2 residues processed: 87 average time/residue: 1.2109 time to fit residues: 109.3429 Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118464 restraints weight = 5037.635| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.17 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4534 Z= 0.217 Angle : 0.595 10.181 6166 Z= 0.293 Chirality : 0.042 0.175 684 Planarity : 0.005 0.046 790 Dihedral : 5.210 47.995 632 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.85 % Allowed : 19.51 % Favored : 77.64 % 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: 0.77 (0.37), residues: 534 helix: 1.46 (0.48), residues: 131 sheet: 0.85 (0.38), residues: 181 loop : -0.28 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.030 0.002 PHE C 43 TYR 0.012 0.001 TYR B 20 ARG 0.007 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8201 (tt0) cc_final: 0.7804 (pt0) REVERT: A 123 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 160 LYS cc_start: 0.8269 (tttt) cc_final: 0.7927 (ttmp) REVERT: A 182 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7961 (mp0) REVERT: B 117 GLU cc_start: 0.7264 (pt0) cc_final: 0.7001 (mm-30) REVERT: B 172 GLU cc_start: 0.5471 (mt-10) cc_final: 0.4866 (tt0) REVERT: B 191 LYS cc_start: 0.8768 (pttp) cc_final: 0.8535 (pttp) REVERT: C 64 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8153 (mt-10) outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 1.1132 time to fit residues: 92.9387 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 97 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN C 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124100 restraints weight = 5068.416| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.08 r_work: 0.3161 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4534 Z= 0.204 Angle : 0.561 10.666 6166 Z= 0.276 Chirality : 0.041 0.168 684 Planarity : 0.004 0.035 790 Dihedral : 4.134 14.875 630 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.66 % Allowed : 18.29 % Favored : 78.05 % 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: 0.75 (0.37), residues: 534 helix: 1.41 (0.48), residues: 131 sheet: 0.88 (0.39), residues: 179 loop : -0.30 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.009 0.001 PHE B 142 TYR 0.007 0.001 TYR A 140 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8309 (tttt) cc_final: 0.8002 (ttmp) REVERT: A 182 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8017 (mp0) REVERT: A 206 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7792 (tm-30) REVERT: B 117 GLU cc_start: 0.7265 (pt0) cc_final: 0.7025 (mm-30) REVERT: B 166 LEU cc_start: 0.8863 (mt) cc_final: 0.8541 (mp) REVERT: B 172 GLU cc_start: 0.5611 (mt-10) cc_final: 0.5124 (tt0) REVERT: B 191 LYS cc_start: 0.8759 (pttp) cc_final: 0.8205 (mmmt) REVERT: C 43 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5443 (t80) REVERT: C 64 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8202 (mt-10) outliers start: 18 outliers final: 7 residues processed: 81 average time/residue: 1.2367 time to fit residues: 104.0786 Evaluate side-chains 73 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 157 GLN B 149 ASN B 160 GLN C 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120098 restraints weight = 5044.101| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.04 r_work: 0.3046 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4534 Z= 0.278 Angle : 0.595 10.894 6166 Z= 0.294 Chirality : 0.043 0.173 684 Planarity : 0.005 0.037 790 Dihedral : 4.314 16.457 630 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.07 % Allowed : 20.33 % Favored : 75.61 % 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 (0.37), residues: 534 helix: 1.44 (0.48), residues: 124 sheet: 0.89 (0.39), residues: 176 loop : -0.39 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.002 PHE C 43 TYR 0.012 0.001 TYR B 20 ARG 0.005 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8088 (tpp) cc_final: 0.7787 (mmm) REVERT: A 123 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7805 (tp) REVERT: A 160 LYS cc_start: 0.8305 (tttt) cc_final: 0.7973 (ttmp) REVERT: A 182 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 59 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: B 166 LEU cc_start: 0.8835 (mt) cc_final: 0.8498 (mp) REVERT: B 191 LYS cc_start: 0.8771 (pttp) cc_final: 0.8217 (mmmt) REVERT: C 43 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.5710 (t80) REVERT: C 64 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8193 (mt-10) outliers start: 20 outliers final: 11 residues processed: 79 average time/residue: 1.1767 time to fit residues: 96.6209 Evaluate side-chains 77 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110507 restraints weight = 5143.089| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.22 r_work: 0.3032 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4534 Z= 0.259 Angle : 0.589 11.156 6166 Z= 0.292 Chirality : 0.043 0.222 684 Planarity : 0.004 0.030 790 Dihedral : 4.305 14.920 630 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.46 % Allowed : 21.75 % Favored : 74.80 % 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: 0.59 (0.37), residues: 534 helix: 1.36 (0.48), residues: 124 sheet: 0.71 (0.38), residues: 181 loop : -0.33 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE C 43 TYR 0.013 0.001 TYR B 20 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7951 (p0) REVERT: A 146 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8461 (tttt) REVERT: A 160 LYS cc_start: 0.8293 (tttt) cc_final: 0.7942 (ttmp) REVERT: A 178 LEU cc_start: 0.8712 (mt) cc_final: 0.8477 (mp) REVERT: A 182 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7956 (mp0) REVERT: A 206 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7782 (tm-30) REVERT: B 166 LEU cc_start: 0.8831 (mt) cc_final: 0.8486 (mp) REVERT: B 191 LYS cc_start: 0.8766 (pttp) cc_final: 0.8131 (mmmt) REVERT: C 43 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.5392 (t80) REVERT: C 64 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8199 (mt-10) outliers start: 17 outliers final: 8 residues processed: 79 average time/residue: 1.2242 time to fit residues: 100.4000 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 50 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122372 restraints weight = 4983.544| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.07 r_work: 0.3085 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4534 Z= 0.175 Angle : 0.544 7.155 6166 Z= 0.271 Chirality : 0.041 0.175 684 Planarity : 0.004 0.029 790 Dihedral : 4.111 15.421 628 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.05 % Allowed : 22.56 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.37), residues: 534 helix: 1.76 (0.49), residues: 120 sheet: 0.80 (0.39), residues: 178 loop : -0.31 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.001 PHE C 43 TYR 0.014 0.001 TYR B 20 ARG 0.004 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8222 (p0) cc_final: 0.7893 (p0) REVERT: A 146 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8445 (tttt) REVERT: A 160 LYS cc_start: 0.8290 (tttt) cc_final: 0.7955 (ttmp) REVERT: A 178 LEU cc_start: 0.8703 (mt) cc_final: 0.8481 (mp) REVERT: A 182 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7944 (mp0) REVERT: B 166 LEU cc_start: 0.8804 (mt) cc_final: 0.8463 (mp) REVERT: B 191 LYS cc_start: 0.8718 (pttp) cc_final: 0.8169 (mmmt) REVERT: C 43 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.5440 (t80) REVERT: C 64 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8138 (mt-10) outliers start: 15 outliers final: 4 residues processed: 83 average time/residue: 1.2008 time to fit residues: 103.5081 Evaluate side-chains 70 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120884 restraints weight = 5014.659| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4534 Z= 0.222 Angle : 0.566 7.526 6166 Z= 0.282 Chirality : 0.041 0.154 684 Planarity : 0.004 0.029 790 Dihedral : 4.149 15.377 628 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 23.78 % Favored : 73.78 % 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: 0.76 (0.37), residues: 534 helix: 1.76 (0.49), residues: 120 sheet: 0.86 (0.38), residues: 176 loop : -0.39 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.011 0.001 PHE C 43 TYR 0.008 0.001 TYR A 140 ARG 0.005 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8418 (tttt) REVERT: A 160 LYS cc_start: 0.8347 (tttt) cc_final: 0.8019 (ttmp) REVERT: A 178 LEU cc_start: 0.8701 (mt) cc_final: 0.8480 (mp) REVERT: A 182 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7948 (mp0) REVERT: A 206 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7775 (tm-30) REVERT: B 166 LEU cc_start: 0.8807 (mt) cc_final: 0.8463 (mp) REVERT: B 191 LYS cc_start: 0.8728 (pttp) cc_final: 0.8181 (mmmt) REVERT: C 43 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.5609 (t80) REVERT: C 64 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8175 (mt-10) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 1.1938 time to fit residues: 93.1384 Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121624 restraints weight = 5027.137| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.07 r_work: 0.3102 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4534 Z= 0.194 Angle : 0.548 7.282 6166 Z= 0.273 Chirality : 0.041 0.147 684 Planarity : 0.004 0.029 790 Dihedral : 4.101 15.457 628 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.85 % Allowed : 23.78 % Favored : 73.37 % 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: 0.83 (0.37), residues: 534 helix: 1.81 (0.50), residues: 120 sheet: 0.91 (0.39), residues: 175 loop : -0.33 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE C 43 TYR 0.012 0.001 TYR B 20 ARG 0.004 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8399 (tttt) REVERT: A 160 LYS cc_start: 0.8349 (tttt) cc_final: 0.8022 (ttmp) REVERT: A 178 LEU cc_start: 0.8691 (mt) cc_final: 0.8477 (mp) REVERT: A 182 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7909 (mp0) REVERT: A 206 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7777 (tm-30) REVERT: B 166 LEU cc_start: 0.8806 (mt) cc_final: 0.8458 (mp) REVERT: B 191 LYS cc_start: 0.8753 (pttp) cc_final: 0.8214 (mmmt) REVERT: C 43 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5609 (t80) REVERT: C 64 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8068 (mt-10) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 1.1727 time to fit residues: 86.7224 Evaluate side-chains 68 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119978 restraints weight = 5024.463| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.09 r_work: 0.3041 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4534 Z= 0.245 Angle : 0.570 7.484 6166 Z= 0.284 Chirality : 0.042 0.161 684 Planarity : 0.004 0.029 790 Dihedral : 4.187 15.475 628 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.03 % Allowed : 24.19 % Favored : 73.78 % 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: 0.73 (0.37), residues: 534 helix: 1.71 (0.49), residues: 120 sheet: 0.84 (0.38), residues: 173 loop : -0.37 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.012 0.001 PHE C 43 TYR 0.015 0.001 TYR B 20 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8492 (tttt) REVERT: A 160 LYS cc_start: 0.8358 (tttt) cc_final: 0.8036 (ttmp) REVERT: A 182 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7937 (mp0) REVERT: A 206 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7786 (tm-30) REVERT: B 166 LEU cc_start: 0.8815 (mt) cc_final: 0.8462 (mp) REVERT: B 191 LYS cc_start: 0.8724 (pttp) cc_final: 0.8142 (mmmt) REVERT: C 43 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.5782 (t80) REVERT: C 64 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8155 (mt-10) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 1.3502 time to fit residues: 96.5121 Evaluate side-chains 66 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116181 restraints weight = 5050.350| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.06 r_work: 0.3094 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4534 Z= 0.178 Angle : 0.540 7.276 6166 Z= 0.268 Chirality : 0.040 0.140 684 Planarity : 0.004 0.029 790 Dihedral : 4.097 18.198 628 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 24.19 % Favored : 73.58 % 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: 0.84 (0.37), residues: 534 helix: 1.84 (0.50), residues: 120 sheet: 0.93 (0.39), residues: 173 loop : -0.34 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.009 0.001 PHE C 43 TYR 0.015 0.001 TYR B 20 ARG 0.002 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8452 (tttt) REVERT: A 160 LYS cc_start: 0.8339 (tttt) cc_final: 0.8003 (ttmp) REVERT: A 182 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7907 (mp0) REVERT: A 206 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7765 (tm-30) REVERT: B 138 TYR cc_start: 0.9025 (p90) cc_final: 0.8804 (p90) REVERT: B 166 LEU cc_start: 0.8797 (mt) cc_final: 0.8447 (mp) REVERT: B 191 LYS cc_start: 0.8745 (pttp) cc_final: 0.8184 (mmmt) REVERT: C 43 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5580 (t80) REVERT: C 64 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8002 (mt-10) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 1.1913 time to fit residues: 87.9809 Evaluate side-chains 69 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119288 restraints weight = 5032.026| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.09 r_work: 0.3046 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4534 Z= 0.271 Angle : 0.587 7.572 6166 Z= 0.293 Chirality : 0.042 0.166 684 Planarity : 0.004 0.031 790 Dihedral : 4.257 17.341 628 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.24 % Allowed : 24.59 % Favored : 73.17 % 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 (0.36), residues: 534 helix: 1.67 (0.49), residues: 120 sheet: 0.67 (0.38), residues: 174 loop : -0.36 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.014 0.001 PHE C 43 TYR 0.015 0.001 TYR B 20 ARG 0.003 0.000 ARG C 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.79 seconds wall clock time: 62 minutes 25.85 seconds (3745.85 seconds total)