Starting phenix.real_space_refine on Wed Mar 5 14:29:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027.map" model { file = "/net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg9_16027/03_2025/8bg9_16027_neut.cif" } resolution = 3.5 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= 0.005 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 6 5.16 5 C 1074 2.51 5 N 300 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 1692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.66, per 1000 atoms: 0.98 Number of scatterers: 1692 At special positions: 0 Unit cell: (86.688, 62.608, 30.1, 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 6 16.00 O 312 8.00 N 300 7.00 C 1074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 190.3 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.43 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: 525 1.34 - 1.46: 483 1.46 - 1.58: 708 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 1728 Sorted by residual: bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.06e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 4.04e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.78e-02 3.16e+03 3.98e+00 bond pdb=" CA SER F 8 " pdb=" CB SER F 8 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.78e-02 3.16e+03 3.92e+00 ... (remaining 1723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 1921 1.78 - 3.56: 323 3.56 - 5.33: 51 5.33 - 7.11: 6 7.11 - 8.89: 9 Bond angle restraints: 2310 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" CA TYR E 10 " pdb=" CB TYR E 10 " ideal model delta sigma weight residual 109.72 118.61 -8.89 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR C 10 " pdb=" CA TYR C 10 " pdb=" CB TYR C 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.64e+01 angle pdb=" C TYR A 10 " pdb=" CA TYR A 10 " pdb=" CB TYR A 10 " ideal model delta sigma weight residual 109.72 118.60 -8.88 1.73e+00 3.34e-01 2.63e+01 angle pdb=" CB GLU F 11 " pdb=" CG GLU F 11 " pdb=" CD GLU F 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" CB GLU D 11 " pdb=" CG GLU D 11 " pdb=" CD GLU D 11 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.70e+00 3.46e-01 2.04e+01 ... (remaining 2305 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.61: 780 11.61 - 23.22: 120 23.22 - 34.82: 42 34.82 - 46.43: 9 46.43 - 58.03: 9 Dihedral angle restraints: 960 sinusoidal: 366 harmonic: 594 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER B 8 " pdb=" C SER B 8 " pdb=" N GLY B 9 " pdb=" CA GLY B 9 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 957 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.045: 87 0.045 - 0.087: 62 0.087 - 0.129: 46 0.129 - 0.171: 24 0.171 - 0.213: 15 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL C 18 " pdb=" N VAL C 18 " pdb=" C VAL C 18 " pdb=" CB VAL C 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 18 " pdb=" N VAL A 18 " pdb=" C VAL A 18 " pdb=" CB VAL A 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL E 18 " pdb=" N VAL E 18 " pdb=" C VAL E 18 " pdb=" CB VAL E 18 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 231 not shown) Planarity restraints: 306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C SER D 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER D 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY D 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 8 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C SER B 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER B 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY B 9 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 8 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.58e+00 pdb=" C SER F 8 " -0.028 2.00e-02 2.50e+03 pdb=" O SER F 8 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY F 9 " 0.009 2.00e-02 2.50e+03 ... (remaining 303 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 809 2.97 - 3.45: 1558 3.45 - 3.93: 2520 3.93 - 4.42: 2733 4.42 - 4.90: 4413 Nonbonded interactions: 12033 Sorted by model distance: nonbonded pdb=" OD1 ASP B 7 " pdb=" N GLY B 9 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP A 7 " pdb=" N GLY A 9 " model vdw 2.484 3.120 nonbonded pdb=" OD1 ASP D 7 " pdb=" N GLY D 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP E 7 " pdb=" N GLY E 9 " model vdw 2.485 3.120 nonbonded pdb=" OD1 ASP C 7 " pdb=" N GLY C 9 " model vdw 2.485 3.120 ... (remaining 12028 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.340 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.008 0.037 1728 Z= 0.474 Angle : 1.465 8.889 2310 Z= 0.953 Chirality : 0.091 0.213 234 Planarity : 0.007 0.043 306 Dihedral : 14.959 58.032 588 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Rotamer: Outliers : 12.50 % Allowed : 23.21 % Favored : 64.29 % 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: -5.16 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS E 6 PHE 0.025 0.006 PHE E 19 TYR 0.020 0.005 TYR D 10 ARG 0.006 0.002 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.189 Fit side-chains REVERT: A 10 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 10 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.6877 (t80) REVERT: C 3 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6864 (tt0) REVERT: C 5 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7350 (ttm110) REVERT: C 10 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6332 (t80) REVERT: D 5 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7383 (mtp180) REVERT: D 10 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6182 (t80) outliers start: 21 outliers final: 11 residues processed: 55 average time/residue: 0.1283 time to fit residues: 8.0990 Evaluate side-chains 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 14 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 15 GLN B 13 HIS C 13 HIS C 14 HIS D 13 HIS D 14 HIS E 13 HIS E 15 GLN F 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.163494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.148061 restraints weight = 2567.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.150999 restraints weight = 1251.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.153052 restraints weight = 791.815| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1728 Z= 0.135 Angle : 0.638 6.088 2310 Z= 0.335 Chirality : 0.051 0.141 234 Planarity : 0.002 0.007 306 Dihedral : 9.363 46.191 257 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 7.74 % Allowed : 8.93 % Favored : 83.33 % 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: -4.79 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.22), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 13 PHE 0.008 0.001 PHE D 19 TYR 0.017 0.003 TYR B 10 ARG 0.001 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.198 Fit side-chains REVERT: A 10 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6571 (t80) REVERT: E 17 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7777 (tt) outliers start: 13 outliers final: 7 residues processed: 29 average time/residue: 0.1382 time to fit residues: 4.7352 Evaluate side-chains 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4633 r_free = 0.4633 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.127692 restraints weight = 2796.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.130205 restraints weight = 1297.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.131885 restraints weight = 818.656| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 1728 Z= 0.361 Angle : 0.846 8.139 2310 Z= 0.452 Chirality : 0.060 0.198 234 Planarity : 0.004 0.019 306 Dihedral : 8.802 55.101 235 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 6.55 % Allowed : 13.69 % Favored : 79.76 % 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: -4.78 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS D 13 PHE 0.017 0.003 PHE D 4 TYR 0.032 0.006 TYR F 10 ARG 0.006 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.203 Fit side-chains REVERT: C 10 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6853 (t80) REVERT: D 5 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7501 (mmm-85) outliers start: 11 outliers final: 8 residues processed: 25 average time/residue: 0.1323 time to fit residues: 4.1733 Evaluate side-chains 23 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 17 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.133536 restraints weight = 2526.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.136384 restraints weight = 1130.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.138290 restraints weight = 707.548| |-----------------------------------------------------------------------------| r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1728 Z= 0.142 Angle : 0.582 5.370 2310 Z= 0.305 Chirality : 0.049 0.138 234 Planarity : 0.002 0.011 306 Dihedral : 7.693 59.486 235 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.17 % Allowed : 16.67 % Favored : 79.17 % 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: -4.34 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.28), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.010 0.002 PHE E 4 TYR 0.019 0.004 TYR B 10 ARG 0.004 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.193 Fit side-chains REVERT: C 8 SER cc_start: 0.8734 (m) cc_final: 0.8295 (t) REVERT: D 8 SER cc_start: 0.8972 (m) cc_final: 0.8647 (t) REVERT: E 1 ASP cc_start: 0.7692 (t0) cc_final: 0.7452 (t0) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.0835 time to fit residues: 2.7457 Evaluate side-chains 21 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.140530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.126996 restraints weight = 2631.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.129659 restraints weight = 1182.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.131427 restraints weight = 733.720| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1728 Z= 0.225 Angle : 0.669 6.885 2310 Z= 0.349 Chirality : 0.052 0.148 234 Planarity : 0.003 0.010 306 Dihedral : 7.688 59.646 233 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.57 % Allowed : 17.86 % Favored : 78.57 % 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: -4.38 (0.38), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 13 PHE 0.010 0.002 PHE B 4 TYR 0.024 0.005 TYR F 10 ARG 0.003 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.189 Fit side-chains REVERT: C 5 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7879 (tpp80) REVERT: D 8 SER cc_start: 0.9244 (m) cc_final: 0.8738 (t) outliers start: 6 outliers final: 6 residues processed: 23 average time/residue: 0.1313 time to fit residues: 3.6519 Evaluate side-chains 21 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.143809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.129496 restraints weight = 2648.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.132325 restraints weight = 1182.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.134168 restraints weight = 730.543| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1728 Z= 0.157 Angle : 0.578 6.947 2310 Z= 0.303 Chirality : 0.049 0.134 234 Planarity : 0.002 0.007 306 Dihedral : 7.313 57.863 233 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.17 % Allowed : 16.67 % Favored : 79.17 % 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: -4.15 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 13 PHE 0.008 0.002 PHE E 4 TYR 0.018 0.004 TYR B 10 ARG 0.002 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.254 Fit side-chains REVERT: C 5 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7907 (tpp80) REVERT: D 8 SER cc_start: 0.9115 (m) cc_final: 0.8758 (t) REVERT: E 10 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.6987 (p90) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.1150 time to fit residues: 3.3893 Evaluate side-chains 21 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4635 r_free = 0.4635 target = 0.140125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.126620 restraints weight = 2695.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.129267 restraints weight = 1210.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.131067 restraints weight = 751.533| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.7369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1728 Z= 0.247 Angle : 0.658 8.182 2310 Z= 0.345 Chirality : 0.051 0.139 234 Planarity : 0.003 0.010 306 Dihedral : 7.800 58.681 233 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 4.17 % Allowed : 19.05 % Favored : 76.79 % 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: -4.31 (0.40), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.30), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 13 PHE 0.011 0.002 PHE B 20 TYR 0.025 0.005 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.185 Fit side-chains REVERT: A 3 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7500 (tt0) REVERT: A 10 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6982 (t80) REVERT: C 5 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8049 (tpp80) REVERT: D 8 SER cc_start: 0.9254 (m) cc_final: 0.8804 (t) REVERT: E 10 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6952 (p90) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.1029 time to fit residues: 3.2621 Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4670 r_free = 0.4670 target = 0.143655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.129448 restraints weight = 2674.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.132292 restraints weight = 1156.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.134172 restraints weight = 709.464| |-----------------------------------------------------------------------------| r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1728 Z= 0.155 Angle : 0.576 6.904 2310 Z= 0.301 Chirality : 0.049 0.128 234 Planarity : 0.002 0.011 306 Dihedral : 7.277 56.543 233 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.17 % Allowed : 19.05 % Favored : 76.79 % 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: -4.12 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.008 0.002 PHE E 4 TYR 0.017 0.003 TYR B 10 ARG 0.002 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.195 Fit side-chains REVERT: A 3 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7446 (tt0) REVERT: B 3 GLU cc_start: 0.7930 (tt0) cc_final: 0.7628 (tt0) REVERT: C 5 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7981 (tpp80) REVERT: D 8 SER cc_start: 0.9216 (m) cc_final: 0.8897 (t) REVERT: E 10 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7041 (p90) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.1276 time to fit residues: 4.0311 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4641 r_free = 0.4641 target = 0.139998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.126030 restraints weight = 2727.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.128775 restraints weight = 1170.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.130573 restraints weight = 715.038| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1728 Z= 0.238 Angle : 0.645 7.314 2310 Z= 0.340 Chirality : 0.051 0.135 234 Planarity : 0.003 0.012 306 Dihedral : 7.724 56.957 233 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 4.17 % Allowed : 19.05 % Favored : 76.79 % 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: -4.30 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 13 PHE 0.010 0.002 PHE D 20 TYR 0.023 0.005 TYR B 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.185 Fit side-chains REVERT: A 3 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7335 (tt0) REVERT: A 10 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6802 (t80) REVERT: B 3 GLU cc_start: 0.7981 (tt0) cc_final: 0.7579 (tt0) REVERT: B 32 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8695 (mp) REVERT: C 5 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8011 (tpp80) REVERT: D 8 SER cc_start: 0.9313 (m) cc_final: 0.8892 (t) REVERT: E 10 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6948 (p90) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.1177 time to fit residues: 3.9762 Evaluate side-chains 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 = 0.4628 r_free = 0.4628 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.126934 restraints weight = 2767.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.129654 restraints weight = 1198.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.131480 restraints weight = 735.515| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 1728 Z= 0.216 Angle : 0.641 7.151 2310 Z= 0.332 Chirality : 0.050 0.137 234 Planarity : 0.002 0.011 306 Dihedral : 7.638 56.488 233 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.36 % Allowed : 18.45 % Favored : 76.19 % 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: -4.26 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.009 0.002 PHE D 20 TYR 0.021 0.004 TYR B 10 ARG 0.001 0.000 ARG C 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.189 Fit side-chains REVERT: A 3 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7479 (tt0) REVERT: A 10 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6942 (t80) REVERT: B 3 GLU cc_start: 0.8079 (tt0) cc_final: 0.7649 (tt0) REVERT: B 32 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8699 (mp) REVERT: D 8 SER cc_start: 0.9295 (m) cc_final: 0.8901 (t) REVERT: E 10 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7009 (p90) outliers start: 9 outliers final: 6 residues processed: 28 average time/residue: 0.0927 time to fit residues: 3.3010 Evaluate side-chains 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.5033 r_free = 0.5033 target = 0.341496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5539 r_free = 0.5539 target = 0.276450 restraints weight = 2356.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5570 r_free = 0.5570 target = 0.278677 restraints weight = 1080.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5584 r_free = 0.5584 target = 0.280028 restraints weight = 601.474| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1728 Z= 0.145 Angle : 0.566 6.203 2310 Z= 0.292 Chirality : 0.048 0.125 234 Planarity : 0.002 0.010 306 Dihedral : 7.197 54.868 233 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.17 % Allowed : 19.05 % Favored : 76.79 % 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: -4.01 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.007 0.002 PHE E 4 TYR 0.016 0.003 TYR B 10 ARG 0.002 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 896.22 seconds wall clock time: 16 minutes 42.95 seconds (1002.95 seconds total)