Starting phenix.real_space_refine on Thu Feb 13 20:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.map" model { file = "/net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x57_33010/02_2025/7x57_33010.cif" } resolution = 3.63 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 242 5.49 5 S 20 5.16 5 C 5373 2.51 5 N 1845 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.80, per 1000 atoms: 0.59 Number of scatterers: 9767 At special positions: 0 Unit cell: (120.75, 93.45, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 242 15.00 O 2287 8.00 N 1845 7.00 C 5373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 638.3 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 78.8% alpha, 2.0% beta 120 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.798A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.517A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.559A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.720A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.812A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 118 through 119 358 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 3371 1.45 - 1.57: 4658 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10418 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG LYS H 77 " pdb=" CD LYS H 77 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB MET B 84 " pdb=" CG MET B 84 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 14651 1.76 - 3.53: 407 3.53 - 5.29: 23 5.29 - 7.06: 3 7.06 - 8.82: 2 Bond angle restraints: 15086 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 104.00 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA ARG H 92 " pdb=" CB ARG H 92 " pdb=" CG ARG H 92 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 angle pdb=" C ALA F 76 " pdb=" N LYS F 77 " pdb=" CA LYS F 77 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.35e+00 angle pdb=" C TYR D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 120.28 116.66 3.62 1.34e+00 5.57e-01 7.31e+00 angle pdb=" N GLY D 56 " pdb=" CA GLY D 56 " pdb=" C GLY D 56 " ideal model delta sigma weight residual 112.50 109.51 2.99 1.16e+00 7.43e-01 6.62e+00 ... (remaining 15081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 4448 34.68 - 69.35: 1165 69.35 - 104.02: 32 104.02 - 138.70: 1 138.70 - 173.37: 3 Dihedral angle restraints: 5649 sinusoidal: 3920 harmonic: 1729 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 46.63 173.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 49.06 170.94 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 50.32 169.68 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 300 0.072 - 0.108: 78 0.108 - 0.143: 14 0.143 - 0.179: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CB VAL H 70 " pdb=" CA VAL H 70 " pdb=" CG1 VAL H 70 " pdb=" CG2 VAL H 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA LYS H 77 " pdb=" N LYS H 77 " pdb=" C LYS H 77 " pdb=" CB LYS H 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB ILE F 50 " pdb=" CA ILE F 50 " pdb=" CG1 ILE F 50 " pdb=" CG2 ILE F 50 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1720 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 67 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG B 67 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG B 67 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP B 68 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 49 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C LEU D 49 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU D 49 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 50 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 67 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ARG D 67 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG D 67 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.022 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2199 2.81 - 3.33: 9187 3.33 - 3.85: 19761 3.85 - 4.38: 21986 4.38 - 4.90: 30534 Nonbonded interactions: 83667 Sorted by model distance: nonbonded pdb=" NE2 GLN A 125 " pdb=" OE2 GLU B 53 " model vdw 2.286 3.120 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DC I 39 " model vdw 2.322 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.337 3.120 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.369 3.120 nonbonded pdb=" N SER A 86 " pdb=" OP1 DT J 7 " model vdw 2.375 3.120 ... (remaining 83662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } 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: 0.240 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.730 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.045 10418 Z= 0.196 Angle : 0.633 8.819 15086 Z= 0.411 Chirality : 0.034 0.179 1723 Planarity : 0.007 0.061 1072 Dihedral : 28.743 173.373 4523 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 579 helix: 0.79 (0.21), residues: 459 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 75 PHE 0.016 0.001 PHE C 84 TYR 0.017 0.001 TYR B 88 ARG 0.011 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8582 (t) cc_final: 0.8232 (m) REVERT: E 64 LYS cc_start: 0.8483 (tptt) cc_final: 0.8135 (tptm) REVERT: F 55 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7792 (mtt180) REVERT: G 86 SER cc_start: 0.8605 (t) cc_final: 0.8132 (p) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3946 time to fit residues: 84.5840 Evaluate side-chains 118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 93 GLN E 125 GLN G 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.163967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116572 restraints weight = 19672.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119952 restraints weight = 11316.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.122128 restraints weight = 8303.255| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10418 Z= 0.394 Angle : 0.695 7.655 15086 Z= 0.394 Chirality : 0.037 0.134 1723 Planarity : 0.005 0.041 1072 Dihedral : 32.474 172.980 3289 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.15 % Allowed : 13.47 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.33), residues: 579 helix: 1.57 (0.23), residues: 471 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS H 75 PHE 0.017 0.002 PHE A 78 TYR 0.016 0.002 TYR B 88 ARG 0.007 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8597 (t) cc_final: 0.8377 (p) REVERT: A 87 SER cc_start: 0.9120 (m) cc_final: 0.8783 (t) REVERT: A 120 MET cc_start: 0.7392 (mmm) cc_final: 0.7186 (mtt) REVERT: F 44 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8293 (mttp) REVERT: G 86 SER cc_start: 0.8772 (t) cc_final: 0.8368 (p) REVERT: G 112 ILE cc_start: 0.9154 (tp) cc_final: 0.8875 (tp) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.3019 time to fit residues: 60.9356 Evaluate side-chains 139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 125 GLN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.166166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123073 restraints weight = 19110.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.125702 restraints weight = 13442.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126383 restraints weight = 10755.908| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10418 Z= 0.190 Angle : 0.575 5.903 15086 Z= 0.340 Chirality : 0.033 0.137 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.225 173.963 3289 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.57 % Allowed : 17.82 % Favored : 79.60 % 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: 2.39 (0.34), residues: 579 helix: 2.33 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.018 0.001 PHE E 67 TYR 0.010 0.001 TYR F 88 ARG 0.005 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8562 (t) cc_final: 0.8331 (p) REVERT: A 90 MET cc_start: 0.7767 (tpp) cc_final: 0.7406 (mpp) REVERT: F 40 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8101 (ttp-170) REVERT: G 86 SER cc_start: 0.8503 (t) cc_final: 0.8216 (p) REVERT: G 112 ILE cc_start: 0.9136 (tp) cc_final: 0.8858 (tp) outliers start: 13 outliers final: 10 residues processed: 137 average time/residue: 0.2766 time to fit residues: 49.8075 Evaluate side-chains 126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 5 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.126941 restraints weight = 19661.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.127686 restraints weight = 14822.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.130114 restraints weight = 13602.031| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.198 Angle : 0.571 7.381 15086 Z= 0.336 Chirality : 0.033 0.154 1723 Planarity : 0.004 0.030 1072 Dihedral : 32.208 174.357 3289 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.37 % Allowed : 20.20 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.34), residues: 579 helix: 2.54 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE C 67 TYR 0.008 0.001 TYR H 72 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.731 Fit side-chains REVERT: A 90 MET cc_start: 0.7815 (tpp) cc_final: 0.7453 (mpp) REVERT: D 84 MET cc_start: 0.6818 (ptt) cc_final: 0.6591 (tpp) REVERT: E 73 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6596 (pt0) REVERT: F 40 ARG cc_start: 0.8242 (mtp180) cc_final: 0.8033 (ttp-170) REVERT: G 86 SER cc_start: 0.8486 (t) cc_final: 0.8196 (p) REVERT: G 112 ILE cc_start: 0.9130 (tp) cc_final: 0.8862 (tp) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.2781 time to fit residues: 47.9036 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.120128 restraints weight = 19565.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123141 restraints weight = 13809.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.123418 restraints weight = 13246.589| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10418 Z= 0.332 Angle : 0.644 7.562 15086 Z= 0.370 Chirality : 0.036 0.157 1723 Planarity : 0.004 0.032 1072 Dihedral : 32.561 177.013 3289 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.95 % Allowed : 22.38 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.34), residues: 579 helix: 2.23 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 75 PHE 0.012 0.002 PHE A 78 TYR 0.010 0.001 TYR B 88 ARG 0.005 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7884 (tpp) cc_final: 0.7584 (tpp) REVERT: B 84 MET cc_start: 0.7523 (tpp) cc_final: 0.7301 (tpp) REVERT: F 44 LYS cc_start: 0.8665 (mmpt) cc_final: 0.8268 (mmtm) REVERT: G 81 ASP cc_start: 0.7253 (t0) cc_final: 0.6929 (t0) REVERT: G 86 SER cc_start: 0.8719 (t) cc_final: 0.8389 (p) REVERT: G 112 ILE cc_start: 0.9172 (tp) cc_final: 0.8941 (tp) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.2841 time to fit residues: 53.0183 Evaluate side-chains 134 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 125 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.165506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.123820 restraints weight = 19707.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.125906 restraints weight = 13351.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.126011 restraints weight = 11561.580| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.211 Angle : 0.590 7.861 15086 Z= 0.345 Chirality : 0.033 0.139 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.323 178.541 3289 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.55 % Allowed : 22.18 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.34), residues: 579 helix: 2.44 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.010 0.001 PHE C 67 TYR 0.008 0.001 TYR D 88 ARG 0.005 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.676 Fit side-chains REVERT: A 90 MET cc_start: 0.7753 (tpp) cc_final: 0.7495 (tpp) REVERT: C 82 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7409 (mt) REVERT: D 84 MET cc_start: 0.6993 (tpp) cc_final: 0.6652 (tpp) REVERT: F 40 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8133 (ttp-170) REVERT: G 81 ASP cc_start: 0.7336 (t0) cc_final: 0.6966 (t0) REVERT: G 86 SER cc_start: 0.8519 (t) cc_final: 0.8184 (p) REVERT: G 112 ILE cc_start: 0.9163 (tp) cc_final: 0.8903 (tp) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2769 time to fit residues: 50.0982 Evaluate side-chains 132 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN E 125 GLN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.164982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.124052 restraints weight = 19825.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.126040 restraints weight = 13609.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126302 restraints weight = 14791.599| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10418 Z= 0.281 Angle : 0.633 10.036 15086 Z= 0.361 Chirality : 0.035 0.150 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.459 179.031 3289 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.95 % Allowed : 24.75 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.34), residues: 579 helix: 2.30 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE E 67 TYR 0.007 0.001 TYR F 88 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.597 Fit side-chains REVERT: C 82 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7405 (mt) REVERT: D 84 MET cc_start: 0.6816 (tpp) cc_final: 0.6523 (tpp) REVERT: F 44 LYS cc_start: 0.8726 (mmpt) cc_final: 0.8259 (mmtm) REVERT: G 86 SER cc_start: 0.8682 (t) cc_final: 0.8343 (p) REVERT: G 112 ILE cc_start: 0.9181 (tp) cc_final: 0.8939 (tp) outliers start: 25 outliers final: 22 residues processed: 133 average time/residue: 0.2592 time to fit residues: 46.0830 Evaluate side-chains 130 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 8 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 125 GLN E 125 GLN G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.129388 restraints weight = 20015.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.131407 restraints weight = 13913.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131903 restraints weight = 14150.459| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.197 Angle : 0.593 9.628 15086 Z= 0.345 Chirality : 0.033 0.142 1723 Planarity : 0.004 0.035 1072 Dihedral : 32.197 179.316 3289 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.15 % Allowed : 24.75 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.34), residues: 579 helix: 2.49 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.007 0.001 PHE E 67 TYR 0.008 0.001 TYR H 72 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.784 Fit side-chains REVERT: C 82 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7288 (mt) REVERT: F 44 LYS cc_start: 0.8734 (mmpt) cc_final: 0.8237 (mmtm) REVERT: G 86 SER cc_start: 0.8432 (t) cc_final: 0.8137 (p) REVERT: G 112 ILE cc_start: 0.9156 (tp) cc_final: 0.8880 (tp) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.2695 time to fit residues: 47.3428 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 125 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.167984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.129087 restraints weight = 20147.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.130351 restraints weight = 13658.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.131005 restraints weight = 13891.366| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.208 Angle : 0.618 11.978 15086 Z= 0.351 Chirality : 0.033 0.152 1723 Planarity : 0.003 0.034 1072 Dihedral : 32.182 178.910 3289 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.16 % Allowed : 26.14 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.35), residues: 579 helix: 2.52 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.78 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.012 0.001 PHE C 78 TYR 0.008 0.001 TYR H 72 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.756 Fit side-chains REVERT: B 84 MET cc_start: 0.7386 (tpp) cc_final: 0.7003 (tpp) REVERT: C 82 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7342 (mt) REVERT: D 84 MET cc_start: 0.6928 (tpp) cc_final: 0.6625 (tpp) REVERT: F 44 LYS cc_start: 0.8711 (mmpt) cc_final: 0.8175 (mmtm) REVERT: G 86 SER cc_start: 0.8394 (t) cc_final: 0.8142 (p) REVERT: G 112 ILE cc_start: 0.9156 (tp) cc_final: 0.8885 (tp) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.2473 time to fit residues: 39.5756 Evaluate side-chains 119 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.167574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.128227 restraints weight = 19826.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.129731 restraints weight = 13063.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.130385 restraints weight = 13494.929| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10418 Z= 0.218 Angle : 0.612 10.627 15086 Z= 0.351 Chirality : 0.033 0.147 1723 Planarity : 0.004 0.037 1072 Dihedral : 32.165 178.642 3289 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.96 % Allowed : 25.74 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.35), residues: 579 helix: 2.47 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -1.85 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 75 PHE 0.012 0.001 PHE E 67 TYR 0.009 0.001 TYR F 88 ARG 0.004 0.000 ARG H 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.690 Fit side-chains REVERT: B 84 MET cc_start: 0.7387 (tpp) cc_final: 0.6894 (tpp) REVERT: C 82 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7332 (mm) REVERT: D 84 MET cc_start: 0.6987 (tpp) cc_final: 0.6676 (tpp) REVERT: F 44 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8146 (mmtm) REVERT: G 86 SER cc_start: 0.8420 (t) cc_final: 0.8203 (p) REVERT: G 112 ILE cc_start: 0.9158 (tp) cc_final: 0.8900 (tp) REVERT: H 84 MET cc_start: 0.7407 (tpp) cc_final: 0.6946 (tpp) outliers start: 20 outliers final: 17 residues processed: 118 average time/residue: 0.2455 time to fit residues: 39.4593 Evaluate side-chains 121 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102439 restraints weight = 19140.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103357 restraints weight = 14999.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.103902 restraints weight = 15164.513| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10418 Z= 0.440 Angle : 0.733 10.796 15086 Z= 0.409 Chirality : 0.039 0.150 1723 Planarity : 0.005 0.034 1072 Dihedral : 32.873 178.142 3289 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.76 % Allowed : 26.34 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.34), residues: 579 helix: 2.02 (0.24), residues: 461 sheet: None (None), residues: 0 loop : -2.23 (0.44), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.026 0.003 PHE C 67 TYR 0.015 0.002 TYR F 88 ARG 0.005 0.001 ARG H 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.63 seconds wall clock time: 44 minutes 55.47 seconds (2695.47 seconds total)