Starting phenix.real_space_refine on Thu Jul 2 16:50:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x57_33010/07_2026/7x57_33010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x57_33010/07_2026/7x57_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_33010/07_2026/7x57_33010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x57_33010/07_2026/7x57_33010.map" model { file = "/net/cci-nas-00/data/ceres_data/7x57_33010/07_2026/7x57_33010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x57_33010/07_2026/7x57_33010.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.21, per 1000 atoms: 0.23 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: 1.09 Conformation dependent library (CDL) restraints added in 200.6 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: 1.45 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: 1.82 Time building geometry restraints manager: 1.38 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' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG J -8 " pdb=" C2' DG J -8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC J -27 " pdb=" C2' DC J -27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT I 55 " pdb=" C2' DT I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.90e+00 bond pdb=" C3' DT I -41 " pdb=" C2' DT I -41 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 14263 1.76 - 3.53: 787 3.53 - 5.29: 31 5.29 - 7.06: 3 7.06 - 8.82: 2 Bond angle restraints: 15086 Sorted by residual: angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 122.81 -2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4' DC I 12 " pdb=" C1' DC I 12 " pdb=" N1 DC I 12 " ideal model delta sigma weight residual 108.00 111.33 -3.33 7.00e-01 2.04e+00 2.26e+01 angle pdb=" O4' DT J 12 " pdb=" C4' DT J 12 " pdb=" C3' DT J 12 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4 DT J 7 " pdb=" C4 DT J 7 " pdb=" C5 DT J 7 " ideal model delta sigma weight residual 124.90 121.78 3.12 7.00e-01 2.04e+00 1.98e+01 angle pdb=" N3 DT J -26 " pdb=" C4 DT J -26 " pdb=" O4 DT J -26 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (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: 1068 0.036 - 0.072: 454 0.072 - 0.108: 167 0.108 - 0.143: 32 0.143 - 0.179: 2 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=" C3' DC I -48 " pdb=" C4' DC I -48 " pdb=" O3' DC I -48 " pdb=" C2' DC I -48 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.91e-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 ... (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: 0.460 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.006 0.035 10418 Z= 0.520 Angle : 0.789 8.819 15086 Z= 0.700 Chirality : 0.045 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.000 ARG F 78 TYR 0.017 0.001 TYR B 88 PHE 0.016 0.001 PHE C 84 HIS 0.004 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.52 (10418) covalent geometry : angle 0.78883 / 0.70 (15086) hydrogen bonds : bond 0.11428 / 7.71 ( 670) hydrogen bonds : angle 4.41167 / 3.19 ( 1671) *********************** 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 : 0.273 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: 0.1807 time to fit residues: 39.0547 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 : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 125 GLN G 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.172590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.132030 restraints weight = 19711.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.134607 restraints weight = 12528.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.134908 restraints weight = 11558.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.135097 restraints weight = 10438.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.135412 restraints weight = 9273.224| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10418 Z= 0.194 Angle : 0.679 9.965 15086 Z= 0.404 Chirality : 0.044 0.273 1723 Planarity : 0.005 0.041 1072 Dihedral : 32.195 174.049 3289 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.16 % Allowed : 13.27 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.33), residues: 579 helix: 1.78 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -1.63 (0.41), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 40 TYR 0.008 0.001 TYR F 72 PHE 0.009 0.002 PHE E 84 HIS 0.007 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (10418) covalent geometry : angle 0.67898 / 0.40 (15086) hydrogen bonds : bond 0.05664 / 3.70 ( 670) hydrogen bonds : angle 3.24336 / 2.32 ( 1671) *********************** 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 164 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8554 (t) cc_final: 0.8306 (p) REVERT: B 84 MET cc_start: 0.7229 (tpp) cc_final: 0.6907 (tpp) REVERT: E 61 LEU cc_start: 0.7961 (mp) cc_final: 0.7758 (mp) REVERT: F 40 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8089 (mtp180) REVERT: F 81 VAL cc_start: 0.7765 (t) cc_final: 0.7335 (t) REVERT: G 86 SER cc_start: 0.8596 (t) cc_final: 0.8205 (p) outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.1320 time to fit residues: 25.6923 Evaluate side-chains 141 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 B residue 54 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 84 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.171399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.130287 restraints weight = 19493.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.132632 restraints weight = 12121.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133264 restraints weight = 11225.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.133612 restraints weight = 9677.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.133733 restraints weight = 8835.783| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10418 Z= 0.157 Angle : 0.626 8.914 15086 Z= 0.379 Chirality : 0.043 0.294 1723 Planarity : 0.004 0.032 1072 Dihedral : 32.292 173.636 3289 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.16 % Allowed : 15.84 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.34), residues: 579 helix: 2.01 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.013 0.001 TYR F 88 PHE 0.023 0.002 PHE C 67 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 (10418) covalent geometry : angle 0.62572 / 0.38 (15086) hydrogen bonds : bond 0.05065 / 3.35 ( 670) hydrogen bonds : angle 3.09400 / 2.21 ( 1671) *********************** 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 147 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8497 (t) cc_final: 0.8217 (p) REVERT: B 84 MET cc_start: 0.7343 (tpp) cc_final: 0.7043 (tpp) REVERT: G 86 SER cc_start: 0.8531 (t) cc_final: 0.8186 (p) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.1309 time to fit residues: 22.8058 Evaluate side-chains 131 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain F residue 30 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 40.0000 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 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 = 0.4589 r_free = 0.4589 target = 0.169697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.127179 restraints weight = 19321.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.128875 restraints weight = 14433.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.129633 restraints weight = 12919.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.130097 restraints weight = 10755.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.130265 restraints weight = 9798.527| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10418 Z= 0.150 Angle : 0.610 7.820 15086 Z= 0.370 Chirality : 0.042 0.300 1723 Planarity : 0.004 0.030 1072 Dihedral : 32.334 174.151 3289 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.76 % Allowed : 18.02 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.35), residues: 579 helix: 2.12 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.009 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (10418) covalent geometry : angle 0.61004 / 0.37 (15086) hydrogen bonds : bond 0.04735 / 3.12 ( 670) hydrogen bonds : angle 2.98195 / 2.14 ( 1671) *********************** 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 143 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8503 (t) cc_final: 0.8276 (p) REVERT: A 90 MET cc_start: 0.7640 (tpp) cc_final: 0.7259 (mpp) REVERT: D 39 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8479 (mmt90) REVERT: G 86 SER cc_start: 0.8541 (t) cc_final: 0.8241 (p) outliers start: 19 outliers final: 15 residues processed: 132 average time/residue: 0.1283 time to fit residues: 22.2135 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.168557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.127540 restraints weight = 19884.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.128730 restraints weight = 14612.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.129541 restraints weight = 15045.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.129800 restraints weight = 12118.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.129993 restraints weight = 12725.022| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10418 Z= 0.182 Angle : 0.632 7.075 15086 Z= 0.375 Chirality : 0.042 0.304 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.454 174.415 3289 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.54 % Allowed : 18.61 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.34), residues: 579 helix: 2.28 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.014 0.002 TYR B 88 PHE 0.007 0.002 PHE E 104 HIS 0.005 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (10418) covalent geometry : angle 0.63175 / 0.38 (15086) hydrogen bonds : bond 0.04868 / 3.17 ( 670) hydrogen bonds : angle 3.05404 / 2.19 ( 1671) *********************** 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 142 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8524 (t) cc_final: 0.8291 (p) REVERT: A 90 MET cc_start: 0.7747 (tpp) cc_final: 0.7399 (mpp) REVERT: G 86 SER cc_start: 0.8566 (t) cc_final: 0.8203 (p) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.1167 time to fit residues: 19.9944 Evaluate side-chains 132 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 VAL 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 71 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 G residue 124 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.170309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128543 restraints weight = 20250.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.130885 restraints weight = 14043.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.131485 restraints weight = 12626.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.131762 restraints weight = 10689.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.132106 restraints weight = 9978.999| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10418 Z= 0.147 Angle : 0.619 10.435 15086 Z= 0.367 Chirality : 0.042 0.310 1723 Planarity : 0.004 0.032 1072 Dihedral : 32.459 174.455 3289 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 20.40 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.35), residues: 579 helix: 2.43 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.010 0.001 TYR D 88 PHE 0.022 0.002 PHE C 67 HIS 0.002 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (10418) covalent geometry : angle 0.61894 / 0.37 (15086) hydrogen bonds : bond 0.04511 / 2.96 ( 670) hydrogen bonds : angle 2.97008 / 2.13 ( 1671) *********************** 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 139 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 86 SER cc_start: 0.8499 (t) cc_final: 0.8272 (p) REVERT: A 90 MET cc_start: 0.7719 (tpp) cc_final: 0.7397 (mpp) REVERT: E 73 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6473 (pt0) REVERT: F 24 ASP cc_start: 0.7751 (t0) cc_final: 0.7397 (t0) REVERT: F 27 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8232 (mp10) REVERT: F 44 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8097 (mttp) REVERT: G 86 SER cc_start: 0.8517 (t) cc_final: 0.8195 (p) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.1242 time to fit residues: 21.1940 Evaluate side-chains 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 C residue 124 ILE 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 62 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU 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 G residue 124 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.169670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.128995 restraints weight = 19890.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130282 restraints weight = 14219.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.131131 restraints weight = 15595.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.131430 restraints weight = 11841.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.131676 restraints weight = 11449.495| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10418 Z= 0.149 Angle : 0.620 8.042 15086 Z= 0.366 Chirality : 0.041 0.309 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.455 174.787 3289 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.56 % Allowed : 22.77 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.35), residues: 579 helix: 2.47 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 40 TYR 0.010 0.001 TYR B 88 PHE 0.008 0.001 PHE E 84 HIS 0.002 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (10418) covalent geometry : angle 0.61964 / 0.37 (15086) hydrogen bonds : bond 0.04453 / 2.91 ( 670) hydrogen bonds : angle 2.93653 / 2.10 ( 1671) *********************** 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 126 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.251 Fit side-chains REVERT: A 90 MET cc_start: 0.7685 (tpp) cc_final: 0.7376 (mpp) REVERT: E 90 MET cc_start: 0.7061 (mmm) cc_final: 0.6839 (tpt) REVERT: F 24 ASP cc_start: 0.7753 (t0) cc_final: 0.7213 (t0) REVERT: F 27 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8210 (mp10) REVERT: F 44 LYS cc_start: 0.8663 (mmpt) cc_final: 0.8287 (mmtm) REVERT: G 86 SER cc_start: 0.8504 (t) cc_final: 0.8173 (p) REVERT: G 112 ILE cc_start: 0.9152 (tp) cc_final: 0.8847 (tp) outliers start: 18 outliers final: 17 residues processed: 120 average time/residue: 0.1188 time to fit residues: 18.9245 Evaluate side-chains 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 C residue 124 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 81 VAL Chi-restraints excluded: chain E residue 73 GLU 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 G residue 124 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 59 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 67 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.129682 restraints weight = 19931.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.131658 restraints weight = 13294.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.132034 restraints weight = 11875.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.132407 restraints weight = 10413.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.132972 restraints weight = 9733.906| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10418 Z= 0.142 Angle : 0.616 11.432 15086 Z= 0.363 Chirality : 0.041 0.311 1723 Planarity : 0.004 0.031 1072 Dihedral : 32.438 175.377 3289 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.56 % Allowed : 23.37 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.35), residues: 579 helix: 2.52 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.009 0.001 TYR H 72 PHE 0.007 0.001 PHE C 67 HIS 0.002 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (10418) covalent geometry : angle 0.61558 / 0.36 (15086) hydrogen bonds : bond 0.04334 / 2.85 ( 670) hydrogen bonds : angle 2.82821 / 2.02 ( 1671) *********************** 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 127 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7675 (tpp) cc_final: 0.7378 (mpp) REVERT: D 84 MET cc_start: 0.7002 (tpp) cc_final: 0.6626 (tpp) REVERT: E 108 ASN cc_start: 0.8319 (t0) cc_final: 0.8102 (t0) REVERT: F 24 ASP cc_start: 0.7699 (t0) cc_final: 0.7171 (t0) REVERT: F 27 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8228 (mp10) REVERT: F 44 LYS cc_start: 0.8699 (mmpt) cc_final: 0.8281 (mppt) REVERT: G 86 SER cc_start: 0.8523 (t) cc_final: 0.8259 (p) REVERT: G 112 ILE cc_start: 0.9122 (tp) cc_final: 0.8850 (tp) outliers start: 18 outliers final: 18 residues processed: 120 average time/residue: 0.1272 time to fit residues: 20.2680 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU 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 G residue 124 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.170165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.129447 restraints weight = 19977.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.130834 restraints weight = 13602.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.131556 restraints weight = 14177.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.131651 restraints weight = 12315.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.132630 restraints weight = 10465.560| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10418 Z= 0.145 Angle : 0.615 9.280 15086 Z= 0.365 Chirality : 0.041 0.311 1723 Planarity : 0.004 0.036 1072 Dihedral : 32.444 175.602 3289 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.37 % Allowed : 23.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.35), residues: 579 helix: 2.57 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.011 0.001 TYR F 88 PHE 0.007 0.001 PHE E 84 HIS 0.002 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (10418) covalent geometry : angle 0.61474 / 0.36 (15086) hydrogen bonds : bond 0.04347 / 2.84 ( 670) hydrogen bonds : angle 2.85457 / 2.03 ( 1671) *********************** 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 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.250 Fit side-chains REVERT: A 90 MET cc_start: 0.7676 (tpp) cc_final: 0.7362 (mpp) REVERT: D 84 MET cc_start: 0.6990 (tpp) cc_final: 0.6608 (tpp) REVERT: F 24 ASP cc_start: 0.7716 (t0) cc_final: 0.7154 (t0) REVERT: F 27 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8258 (mp10) REVERT: G 86 SER cc_start: 0.8528 (t) cc_final: 0.8268 (p) REVERT: G 112 ILE cc_start: 0.9121 (tp) cc_final: 0.8857 (tp) outliers start: 17 outliers final: 17 residues processed: 122 average time/residue: 0.1157 time to fit residues: 18.9397 Evaluate side-chains 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 C residue 124 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 73 GLU 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 G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.170011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.129346 restraints weight = 19826.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.130849 restraints weight = 13482.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132181 restraints weight = 12781.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.132519 restraints weight = 10320.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.132581 restraints weight = 10324.815| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10418 Z= 0.148 Angle : 0.621 7.007 15086 Z= 0.368 Chirality : 0.041 0.312 1723 Planarity : 0.004 0.053 1072 Dihedral : 32.461 175.965 3289 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.76 % Allowed : 22.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.35), residues: 579 helix: 2.55 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.65 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.010 0.001 TYR F 88 PHE 0.018 0.002 PHE C 67 HIS 0.002 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (10418) covalent geometry : angle 0.62094 / 0.37 (15086) hydrogen bonds : bond 0.04312 / 2.82 ( 670) hydrogen bonds : angle 2.88024 / 2.05 ( 1671) ********************** 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 127 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.252 Fit side-chains REVERT: A 90 MET cc_start: 0.7706 (tpp) cc_final: 0.7406 (mpp) REVERT: D 84 MET cc_start: 0.6989 (tpp) cc_final: 0.6664 (tpp) REVERT: F 24 ASP cc_start: 0.7743 (t0) cc_final: 0.7270 (t0) REVERT: F 27 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8201 (mp10) REVERT: G 86 SER cc_start: 0.8525 (t) cc_final: 0.8275 (p) REVERT: G 112 ILE cc_start: 0.9125 (tp) cc_final: 0.8859 (tp) outliers start: 19 outliers final: 18 residues processed: 120 average time/residue: 0.1172 time to fit residues: 18.7961 Evaluate side-chains 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 C residue 124 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU 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 G residue 124 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 79 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.169027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128751 restraints weight = 19932.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130435 restraints weight = 14307.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.131002 restraints weight = 14967.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.131427 restraints weight = 11906.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.131762 restraints weight = 11514.052| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10418 Z= 0.163 Angle : 0.641 12.483 15086 Z= 0.373 Chirality : 0.041 0.313 1723 Planarity : 0.004 0.049 1072 Dihedral : 32.496 176.206 3289 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.37 % Allowed : 24.55 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.35), residues: 579 helix: 2.41 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.009 0.001 TYR F 88 PHE 0.041 0.002 PHE E 67 HIS 0.003 0.001 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (10418) covalent geometry : angle 0.64097 / 0.37 (15086) hydrogen bonds : bond 0.04412 / 2.86 ( 670) hydrogen bonds : angle 2.93251 / 2.09 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.33 seconds wall clock time: 26 minutes 20.65 seconds (1580.65 seconds total)