Starting phenix.real_space_refine on Wed Mar 5 23:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9v_51158/03_2025/9g9v_51158.cif" } resolution = 3.32 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= 0.001 sd= 0.032 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 K 5 8.98 5 S 32 5.16 5 C 2692 2.51 5 N 652 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4073 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1964 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 256} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 75 Unusual residues: {' K': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Restraints were copied for chains: B Time building chain proxies: 3.77, per 1000 atoms: 0.93 Number of scatterers: 4073 At special positions: 0 Unit cell: (62.4, 79.04, 96.512, 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) K 5 19.00 S 32 16.00 O 692 8.00 N 652 7.00 C 2692 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: 1.11 Conformation dependent library (CDL) restraints added in 467.7 milliseconds 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.361A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 4.169A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 52 removed outlier: 3.563A pdb=" N VAL B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 4.169A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 1008 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: 1.12 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: 1.20 - 1.32: 622 1.32 - 1.44: 1160 1.44 - 1.56: 2336 1.56 - 1.68: 0 1.68 - 1.80: 50 Bond restraints: 4168 Sorted by residual: bond pdb=" CG1 ILE B 118 " pdb=" CD1 ILE B 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CG1 ILE A 118 " pdb=" CD1 ILE A 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CB THR A 198 " pdb=" CG2 THR A 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CB THR B 198 " pdb=" CG2 THR B 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG1 ILE B 94 " pdb=" CD1 ILE B 94 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 ... (remaining 4163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 5073 1.10 - 2.20: 499 2.20 - 3.30: 62 3.30 - 4.40: 28 4.40 - 5.50: 12 Bond angle restraints: 5674 Sorted by residual: angle pdb=" C LEU A 29 " pdb=" N GLU A 30 " pdb=" CA GLU A 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" C LEU B 29 " pdb=" N GLU B 30 " pdb=" CA GLU B 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" N GLU B 30 " pdb=" CA GLU B 30 " pdb=" C GLU B 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" N GLU A 30 " pdb=" CA GLU A 30 " pdb=" C GLU A 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" N THR B 210 " ideal model delta sigma weight residual 114.76 117.65 -2.89 1.14e+00 7.69e-01 6.41e+00 ... (remaining 5669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2416 15.06 - 30.12: 134 30.12 - 45.18: 36 45.18 - 60.24: 12 60.24 - 75.30: 4 Dihedral angle restraints: 2602 sinusoidal: 1088 harmonic: 1514 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL B 243 " pdb=" C VAL B 243 " pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta harmonic sigma weight residual 180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2599 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 356 0.037 - 0.073: 205 0.073 - 0.109: 85 0.109 - 0.145: 10 0.145 - 0.181: 8 Chirality restraints: 664 Sorted by residual: chirality pdb=" CA GLU A 30 " pdb=" N GLU A 30 " pdb=" C GLU A 30 " pdb=" CB GLU A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU B 30 " pdb=" N GLU B 30 " pdb=" C GLU B 30 " pdb=" CB GLU B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 661 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 24 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA B 24 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 24 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 25 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 24 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA A 24 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 24 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 85 " 0.010 2.00e-02 2.50e+03 1.43e-02 4.07e+00 pdb=" CG TYR A 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 85 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 85 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 85 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 85 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.82: 1118 2.82 - 3.40: 4864 3.40 - 3.98: 7465 3.98 - 4.56: 10505 4.56 - 5.14: 15075 Nonbonded interactions: 39027 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER B 83 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 83 " pdb=" OD1 ASP B 27 " model vdw 2.245 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 93 " model vdw 2.445 3.040 ... (remaining 39022 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 261 or resid 301 through 302)) selection = chain 'B' } 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: 0.730 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: 0.030 Set scattering table: 0.040 Process input model: 14.900 Find NCS groups from input model: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 0.070 4168 Z= 0.461 Angle : 0.749 5.498 5674 Z= 0.459 Chirality : 0.052 0.181 664 Planarity : 0.005 0.024 684 Dihedral : 11.166 75.301 1634 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.53 % Allowed : 1.05 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.34), residues: 518 helix: 0.30 (0.22), residues: 412 sheet: None (None), residues: 0 loop : -0.95 (0.70), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 78 HIS 0.003 0.001 HIS A 98 PHE 0.021 0.002 PHE A 202 TYR 0.021 0.004 TYR A 85 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8091 (tp30) cc_final: 0.7834 (tp30) REVERT: A 76 VAL cc_start: 0.8447 (m) cc_final: 0.8062 (p) REVERT: A 168 MET cc_start: 0.6991 (tpp) cc_final: 0.6595 (tpp) REVERT: A 255 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7871 (ttp80) REVERT: B 38 GLU cc_start: 0.8097 (tp30) cc_final: 0.7839 (tp30) REVERT: B 76 VAL cc_start: 0.8444 (m) cc_final: 0.8056 (p) REVERT: B 168 MET cc_start: 0.6996 (tpp) cc_final: 0.6594 (tpp) REVERT: B 255 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7876 (ttp80) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2778 time to fit residues: 27.9608 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.146611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101345 restraints weight = 4753.731| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.63 r_work: 0.2798 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4168 Z= 0.284 Angle : 0.544 5.130 5674 Z= 0.309 Chirality : 0.041 0.172 664 Planarity : 0.004 0.024 684 Dihedral : 6.633 46.480 850 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.58 % Allowed : 7.37 % Favored : 91.05 % 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: 2.93 (0.37), residues: 518 helix: 2.49 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.54 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 78 HIS 0.001 0.001 HIS B 98 PHE 0.014 0.001 PHE A 109 TYR 0.013 0.002 TYR A 138 ARG 0.005 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.440 Fit side-chains REVERT: A 38 GLU cc_start: 0.8114 (tp30) cc_final: 0.7861 (tp30) REVERT: A 76 VAL cc_start: 0.8477 (m) cc_final: 0.8142 (p) REVERT: A 141 LYS cc_start: 0.7912 (tttt) cc_final: 0.7425 (tptt) REVERT: A 142 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.6746 (ttm-80) REVERT: B 38 GLU cc_start: 0.8116 (tp30) cc_final: 0.7864 (tp30) REVERT: B 76 VAL cc_start: 0.8479 (m) cc_final: 0.8140 (p) REVERT: B 141 LYS cc_start: 0.7910 (tttt) cc_final: 0.7423 (tptt) REVERT: B 142 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.6743 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.2564 time to fit residues: 23.1610 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.150079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104535 restraints weight = 4734.491| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.63 r_work: 0.2898 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4168 Z= 0.179 Angle : 0.474 4.972 5674 Z= 0.263 Chirality : 0.037 0.145 664 Planarity : 0.003 0.021 684 Dihedral : 5.967 44.600 850 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.84 % Allowed : 7.63 % Favored : 90.53 % 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: 3.70 (0.37), residues: 518 helix: 3.10 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.65 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 78 HIS 0.001 0.000 HIS A 33 PHE 0.013 0.001 PHE B 109 TYR 0.012 0.002 TYR B 138 ARG 0.005 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8006 (tp30) cc_final: 0.7721 (tp30) REVERT: A 76 VAL cc_start: 0.8616 (m) cc_final: 0.8333 (p) REVERT: A 141 LYS cc_start: 0.7991 (tttt) cc_final: 0.7562 (tptt) REVERT: A 168 MET cc_start: 0.6867 (tpp) cc_final: 0.6659 (tpp) REVERT: B 38 GLU cc_start: 0.8009 (tp30) cc_final: 0.7724 (tp30) REVERT: B 76 VAL cc_start: 0.8615 (m) cc_final: 0.8334 (p) REVERT: B 141 LYS cc_start: 0.7996 (tttt) cc_final: 0.7565 (tptt) REVERT: B 168 MET cc_start: 0.6874 (tpp) cc_final: 0.6666 (tpp) outliers start: 7 outliers final: 3 residues processed: 83 average time/residue: 0.2830 time to fit residues: 26.9897 Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.147990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102562 restraints weight = 4752.553| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.59 r_work: 0.2826 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4168 Z= 0.196 Angle : 0.485 5.039 5674 Z= 0.267 Chirality : 0.037 0.143 664 Planarity : 0.003 0.020 684 Dihedral : 5.800 49.414 850 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.32 % Allowed : 9.21 % Favored : 89.47 % 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: 3.99 (0.37), residues: 518 helix: 3.29 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.45 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 PHE 0.013 0.001 PHE A 109 TYR 0.017 0.002 TYR A 138 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7946 (tp30) cc_final: 0.7667 (tp30) REVERT: A 168 MET cc_start: 0.6880 (tpp) cc_final: 0.6671 (tpp) REVERT: B 38 GLU cc_start: 0.7951 (tp30) cc_final: 0.7674 (tp30) REVERT: B 168 MET cc_start: 0.6884 (tpp) cc_final: 0.6676 (tpp) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2535 time to fit residues: 23.2805 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.0070 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.149095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102214 restraints weight = 4903.593| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.70 r_work: 0.2854 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4168 Z= 0.188 Angle : 0.498 7.690 5674 Z= 0.264 Chirality : 0.037 0.144 664 Planarity : 0.003 0.019 684 Dihedral : 5.718 54.045 850 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.32 % Allowed : 11.32 % Favored : 87.37 % 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: 4.19 (0.37), residues: 518 helix: 3.39 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.19 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 PHE 0.013 0.001 PHE A 109 TYR 0.017 0.002 TYR A 138 ARG 0.005 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6902 (tpp) cc_final: 0.6692 (tpp) REVERT: B 168 MET cc_start: 0.6909 (tpp) cc_final: 0.6701 (tpp) outliers start: 5 outliers final: 5 residues processed: 81 average time/residue: 0.2413 time to fit residues: 22.8929 Evaluate side-chains 81 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.145945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099002 restraints weight = 4876.073| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.60 r_work: 0.2879 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4168 Z= 0.202 Angle : 0.502 5.936 5674 Z= 0.270 Chirality : 0.037 0.146 664 Planarity : 0.003 0.021 684 Dihedral : 5.755 59.386 850 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.11 % Allowed : 10.53 % Favored : 87.37 % 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: 4.11 (0.37), residues: 518 helix: 3.38 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.46 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.019 0.001 PHE B 109 TYR 0.013 0.002 TYR B 138 ARG 0.005 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7035 (tpp) cc_final: 0.6811 (tpp) REVERT: B 168 MET cc_start: 0.7032 (tpp) cc_final: 0.6810 (tpp) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2344 time to fit residues: 21.9764 Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.146645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099011 restraints weight = 4867.716| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.61 r_work: 0.2869 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4168 Z= 0.221 Angle : 0.515 5.581 5674 Z= 0.278 Chirality : 0.037 0.152 664 Planarity : 0.003 0.022 684 Dihedral : 5.673 56.882 850 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.58 % Allowed : 10.53 % Favored : 87.89 % 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: 4.06 (0.37), residues: 518 helix: 3.37 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.58 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 PHE 0.021 0.001 PHE B 109 TYR 0.015 0.002 TYR A 138 ARG 0.005 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7054 (tpp) cc_final: 0.6822 (tpp) REVERT: B 168 MET cc_start: 0.7051 (tpp) cc_final: 0.6822 (tpp) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.2496 time to fit residues: 22.9963 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.145578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097454 restraints weight = 4825.755| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.59 r_work: 0.2852 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4168 Z= 0.268 Angle : 0.549 5.444 5674 Z= 0.296 Chirality : 0.039 0.171 664 Planarity : 0.003 0.021 684 Dihedral : 5.659 52.815 850 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.58 % Allowed : 10.53 % Favored : 87.89 % 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: 3.95 (0.37), residues: 518 helix: 3.30 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.67 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 78 HIS 0.001 0.000 HIS B 98 PHE 0.021 0.001 PHE B 109 TYR 0.014 0.002 TYR A 138 ARG 0.005 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7038 (tpp) cc_final: 0.6794 (tpp) REVERT: B 168 MET cc_start: 0.7041 (tpp) cc_final: 0.6798 (tpp) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.2616 time to fit residues: 25.1372 Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.147563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101612 restraints weight = 4797.803| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.61 r_work: 0.2873 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4168 Z= 0.215 Angle : 0.520 5.821 5674 Z= 0.280 Chirality : 0.037 0.170 664 Planarity : 0.003 0.023 684 Dihedral : 5.453 48.243 850 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.58 % Allowed : 10.00 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.02 (0.37), residues: 518 helix: 3.37 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.74 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 78 HIS 0.001 0.000 HIS A 98 PHE 0.020 0.001 PHE A 109 TYR 0.014 0.001 TYR A 138 ARG 0.006 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6895 (tpp) cc_final: 0.6663 (tpp) REVERT: B 168 MET cc_start: 0.6911 (tpp) cc_final: 0.6678 (tpp) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.2453 time to fit residues: 22.9535 Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.146195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.099591 restraints weight = 4860.542| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.56 r_work: 0.2886 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4168 Z= 0.212 Angle : 0.540 5.956 5674 Z= 0.288 Chirality : 0.037 0.167 664 Planarity : 0.003 0.023 684 Dihedral : 5.369 44.127 850 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.58 % Allowed : 9.47 % Favored : 88.95 % 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: 4.04 (0.37), residues: 518 helix: 3.39 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.78 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 78 HIS 0.001 0.000 HIS B 33 PHE 0.020 0.001 PHE A 109 TYR 0.013 0.002 TYR A 138 ARG 0.006 0.001 ARG B 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.7985 (tttt) cc_final: 0.7498 (tptt) REVERT: A 168 MET cc_start: 0.6996 (tpp) cc_final: 0.6766 (tpp) REVERT: B 141 LYS cc_start: 0.7987 (tttt) cc_final: 0.7500 (tptt) REVERT: B 168 MET cc_start: 0.7001 (tpp) cc_final: 0.6773 (tpp) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.2549 time to fit residues: 23.2181 Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.147952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100743 restraints weight = 4847.972| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.58 r_work: 0.2903 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4168 Z= 0.197 Angle : 0.537 6.055 5674 Z= 0.286 Chirality : 0.037 0.162 664 Planarity : 0.003 0.023 684 Dihedral : 5.356 42.209 850 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.32 % Allowed : 10.26 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.09 (0.37), residues: 518 helix: 3.42 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.76 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 78 HIS 0.001 0.000 HIS B 33 PHE 0.020 0.001 PHE B 109 TYR 0.014 0.001 TYR B 138 ARG 0.006 0.001 ARG B 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.63 seconds wall clock time: 37 minutes 43.13 seconds (2263.13 seconds total)