Starting phenix.real_space_refine on Mon Feb 10 19:37:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg9_16027/02_2025/8bg9_16027_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg9_16027/02_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_16027/02_2025/8bg9_16027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg9_16027/02_2025/8bg9_16027.map" model { file = "/net/cci-nas-00/data/ceres_data/8bg9_16027/02_2025/8bg9_16027_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg9_16027/02_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-5592/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: 1.71, per 1000 atoms: 1.01 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: 0.45 Conformation dependent library (CDL) restraints added in 203.7 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: 0.35 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: 0.48 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.190 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- 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 : 0.186 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: 0.1311 time to fit residues: 8.2644 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 : 0.198 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4840 r_free = 0.4840 target = 0.153170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.138123 restraints weight = 2459.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.141104 restraints weight = 1098.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.143147 restraints weight = 671.264| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1728 Z= 0.133 Angle : 0.642 6.233 2310 Z= 0.335 Chirality : 0.052 0.139 234 Planarity : 0.002 0.008 306 Dihedral : 9.553 45.162 257 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.33 % Allowed : 8.93 % Favored : 82.74 % 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: -4.75 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 13 PHE 0.008 0.001 PHE D 19 TYR 0.019 0.004 TYR B 10 ARG 0.002 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 32 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.171 Fit side-chains REVERT: A 10 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6556 (t80) REVERT: C 3 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7067 (tt0) REVERT: E 17 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7813 (tt) outliers start: 14 outliers final: 7 residues processed: 31 average time/residue: 0.1284 time to fit residues: 4.6795 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 : 0.170 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.141613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.127335 restraints weight = 2837.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.130027 restraints weight = 1310.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.131764 restraints weight = 819.291| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 1728 Z= 0.267 Angle : 0.798 6.906 2310 Z= 0.427 Chirality : 0.057 0.194 234 Planarity : 0.004 0.017 306 Dihedral : 8.530 56.338 235 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.95 % Allowed : 15.48 % 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: -4.58 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 13 PHE 0.015 0.003 PHE A 4 TYR 0.032 0.006 TYR B 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 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.145 Fit side-chains REVERT: D 5 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7371 (mmm-85) outliers start: 10 outliers final: 6 residues processed: 24 average time/residue: 0.1074 time to fit residues: 3.1631 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 : 0.199 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.4607 r_free = 0.4607 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.129440 restraints weight = 2664.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.132206 restraints weight = 1236.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.134018 restraints weight = 781.662| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 1728 Z= 0.205 Angle : 0.667 7.914 2310 Z= 0.346 Chirality : 0.052 0.150 234 Planarity : 0.002 0.009 306 Dihedral : 7.428 58.875 233 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % 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: -4.37 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.28), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.011 0.002 PHE D 20 TYR 0.020 0.004 TYR B 10 ARG 0.004 0.000 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 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.189 Fit side-chains REVERT: A 10 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6812 (t80) REVERT: D 8 SER cc_start: 0.8983 (m) cc_final: 0.8769 (t) outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.0671 time to fit residues: 2.2513 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 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4621 r_free = 0.4621 target = 0.139859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.126220 restraints weight = 2631.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.128785 restraints weight = 1188.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.130523 restraints weight = 745.254| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 1728 Z= 0.275 Angle : 0.721 8.268 2310 Z= 0.376 Chirality : 0.053 0.152 234 Planarity : 0.003 0.011 306 Dihedral : 7.923 59.642 233 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.76 % Allowed : 20.83 % Favored : 74.40 % 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: -4.43 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 13 PHE 0.012 0.002 PHE B 20 TYR 0.026 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 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.196 Fit side-chains REVERT: A 10 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6869 (t80) REVERT: C 10 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7024 (t80) REVERT: D 8 SER cc_start: 0.9212 (m) cc_final: 0.8732 (t) outliers start: 8 outliers final: 6 residues processed: 23 average time/residue: 0.0992 time to fit residues: 2.8833 Evaluate side-chains 24 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 8 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: 10.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.138218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.124270 restraints weight = 2747.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.126879 restraints weight = 1198.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.128647 restraints weight = 742.371| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 1728 Z= 0.261 Angle : 0.693 7.692 2310 Z= 0.360 Chirality : 0.053 0.149 234 Planarity : 0.003 0.014 306 Dihedral : 7.826 58.348 233 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.76 % Allowed : 21.43 % Favored : 73.81 % 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: -4.44 (0.38), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 13 PHE 0.010 0.002 PHE B 20 TYR 0.023 0.005 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 27 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.194 Fit side-chains REVERT: A 3 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7456 (tt0) REVERT: A 10 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6877 (t80) REVERT: B 3 GLU cc_start: 0.7946 (tt0) cc_final: 0.7521 (tt0) REVERT: D 8 SER cc_start: 0.9246 (m) cc_final: 0.8844 (t) outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0999 time to fit residues: 3.0429 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 : 0.173 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 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 = 0.4627 r_free = 0.4627 target = 0.139655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.125554 restraints weight = 2685.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.128255 restraints weight = 1214.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.130047 restraints weight = 758.947| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 1728 Z= 0.233 Angle : 0.660 6.538 2310 Z= 0.344 Chirality : 0.052 0.145 234 Planarity : 0.003 0.012 306 Dihedral : 7.611 57.054 233 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 5.36 % Allowed : 22.02 % Favored : 72.62 % 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: -4.40 (0.39), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.30), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.011 0.002 PHE A 4 TYR 0.022 0.004 TYR B 10 ARG 0.002 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: 9 poor density : 17 time to evaluate : 0.184 Fit side-chains REVERT: A 3 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7482 (tt0) REVERT: A 10 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 32 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 5 ARG cc_start: 0.8234 (ttm110) cc_final: 0.8026 (tpp80) REVERT: C 10 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.7034 (t80) REVERT: D 8 SER cc_start: 0.9233 (m) cc_final: 0.8896 (t) REVERT: E 10 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6988 (p90) outliers start: 9 outliers final: 5 residues processed: 25 average time/residue: 0.1006 time to fit residues: 3.1650 Evaluate side-chains 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.4663 r_free = 0.4663 target = 0.143684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.129284 restraints weight = 2714.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.132115 restraints weight = 1195.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.133962 restraints weight = 734.558| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.7720 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= 0.159 Angle : 0.586 5.413 2310 Z= 0.304 Chirality : 0.049 0.135 234 Planarity : 0.002 0.009 306 Dihedral : 7.188 55.311 233 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.76 % Allowed : 20.24 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.41), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (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 B 19 TYR 0.018 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: 8 poor density : 18 time to evaluate : 0.193 Fit side-chains REVERT: A 3 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7416 (tt0) REVERT: D 8 SER cc_start: 0.9127 (m) cc_final: 0.8901 (t) REVERT: E 10 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7093 (p90) outliers start: 8 outliers final: 6 residues processed: 25 average time/residue: 0.1020 time to fit residues: 3.1783 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 : 0.194 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.148056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.133242 restraints weight = 2704.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.136196 restraints weight = 1204.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.138175 restraints weight = 740.464| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1728 Z= 0.111 Angle : 0.521 4.745 2310 Z= 0.271 Chirality : 0.047 0.120 234 Planarity : 0.001 0.009 306 Dihedral : 6.756 53.063 233 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.98 % Allowed : 21.43 % Favored : 75.60 % 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: -3.96 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.008 0.001 PHE B 19 TYR 0.013 0.003 TYR B 10 ARG 0.002 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 26 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.222 Fit side-chains REVERT: A 3 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7392 (tt0) REVERT: C 8 SER cc_start: 0.8934 (m) cc_final: 0.8703 (t) REVERT: E 10 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7425 (p90) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.0957 time to fit residues: 3.1933 Evaluate side-chains 25 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 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 = 0.4645 r_free = 0.4645 target = 0.140771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.126739 restraints weight = 2790.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.129427 restraints weight = 1210.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.131248 restraints weight = 743.082| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.7816 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= 0.246 Angle : 0.643 5.884 2310 Z= 0.338 Chirality : 0.051 0.135 234 Planarity : 0.003 0.011 306 Dihedral : 7.528 55.585 233 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.36 % Allowed : 19.64 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.41), 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 0.007 0.003 HIS B 13 PHE 0.010 0.002 PHE A 4 TYR 0.023 0.004 TYR B 10 ARG 0.002 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 28 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.185 Fit side-chains REVERT: A 3 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7409 (tt0) REVERT: A 10 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6873 (t80) REVERT: B 32 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 10 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6925 (p90) outliers start: 9 outliers final: 6 residues processed: 26 average time/residue: 0.0826 time to fit residues: 2.9015 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 : 0.210 ------------------------------------------------------------------------------- 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: 0.0970 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.5038 r_free = 0.5038 target = 0.337014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5531 r_free = 0.5531 target = 0.273588 restraints weight = 2339.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.275838 restraints weight = 1082.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5579 r_free = 0.5579 target = 0.277276 restraints weight = 612.648| |-----------------------------------------------------------------------------| r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7968 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= 0.131 Angle : 0.540 5.003 2310 Z= 0.281 Chirality : 0.047 0.123 234 Planarity : 0.001 0.008 306 Dihedral : 6.936 53.467 233 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.57 % Allowed : 22.02 % Favored : 74.40 % 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 (0.43), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.008 0.002 PHE B 19 TYR 0.015 0.003 TYR B 10 ARG 0.001 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 885.25 seconds wall clock time: 16 minutes 46.57 seconds (1006.57 seconds total)