Starting phenix.real_space_refine on Wed Jul 30 07:12:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.map" model { file = "/net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wz5_21970/07_2025/6wz5_21970.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 306 5.49 5 S 12 5.16 5 C 6860 2.51 5 N 2349 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3155 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3118 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Time building chain proxies: 9.17, per 1000 atoms: 0.74 Number of scatterers: 12443 At special positions: 0 Unit cell: (74.2, 116.6, 122.96, 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 12 16.00 P 306 15.00 O 2916 8.00 N 2349 7.00 C 6860 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: 3.00 Conformation dependent library (CDL) restraints added in 950.5 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 3.1% beta 153 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.743A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.987A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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 removed outlier: 3.706A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.773A 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 'B' and resid 96 through 98 removed outlier: 6.695A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.928A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.556A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.789A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 392 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1867 1.32 - 1.44: 4639 1.44 - 1.56: 6148 1.56 - 1.68: 610 1.68 - 1.80: 22 Bond restraints: 13286 Sorted by residual: bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.339 1.251 0.088 5.57e-02 3.22e+02 2.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.379 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 ... (remaining 13281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18574 1.71 - 3.43: 654 3.43 - 5.14: 15 5.14 - 6.85: 4 6.85 - 8.57: 2 Bond angle restraints: 19249 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.95 -5.77 2.37e+00 1.78e-01 5.93e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.83 -3.63 1.50e+00 4.44e-01 5.84e+00 angle pdb=" C3' DC I -26 " pdb=" C2' DC I -26 " pdb=" C1' DC I -26 " ideal model delta sigma weight residual 101.60 98.31 3.29 1.50e+00 4.44e-01 4.82e+00 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.14 117.37 3.77 1.75e+00 3.27e-01 4.63e+00 angle pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " pdb=" C1' DC I -25 " ideal model delta sigma weight residual 101.60 98.43 3.17 1.50e+00 4.44e-01 4.46e+00 ... (remaining 19244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5548 33.12 - 66.24: 1634 66.24 - 99.36: 32 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 7216 sinusoidal: 4964 harmonic: 2252 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.87 139.13 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1149 0.030 - 0.060: 710 0.060 - 0.090: 252 0.090 - 0.119: 63 0.119 - 0.149: 18 Chirality restraints: 2192 Sorted by residual: chirality pdb=" C4' DA J -35 " pdb=" C5' DA J -35 " pdb=" O4' DA J -35 " pdb=" C3' DA J -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ARG H 76 " pdb=" N ARG H 76 " pdb=" C ARG H 76 " pdb=" CB ARG H 76 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C4' DA I 26 " pdb=" C5' DA I 26 " pdb=" O4' DA I 26 " pdb=" C3' DA I 26 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2189 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 43 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.026 2.00e-02 2.50e+03 1.19e-02 3.92e+00 pdb=" N9 DA I 26 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2451 2.78 - 3.31: 10584 3.31 - 3.84: 26079 3.84 - 4.37: 31295 4.37 - 4.90: 42128 Nonbonded interactions: 112537 Sorted by model distance: nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.253 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.320 3.120 nonbonded pdb=" N2 DG I 38 " pdb=" O2 DC J -38 " model vdw 2.329 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.366 3.040 ... (remaining 112532 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.650 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.810 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 13286 Z= 0.373 Angle : 0.693 8.565 19249 Z= 0.424 Chirality : 0.043 0.149 2192 Planarity : 0.005 0.051 1372 Dihedral : 28.628 165.601 5760 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 3.24 % Favored : 95.83 % 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: -0.00 (0.27), residues: 758 helix: 0.51 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE A 67 TYR 0.014 0.002 TYR G 57 ARG 0.006 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.08467 ( 806) hydrogen bonds : angle 3.42209 ( 1998) covalent geometry : bond 0.00837 (13286) covalent geometry : angle 0.69294 (19249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.887 Fit side-chains REVERT: G 15 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7220 (mtpt) REVERT: G 24 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7781 (mm-40) REVERT: H 68 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6886 (mp0) outliers start: 6 outliers final: 2 residues processed: 196 average time/residue: 1.8881 time to fit residues: 390.3900 Evaluate side-chains 149 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 31 HIS C 104 GLN D 92 GLN E 68 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 44 GLN H 92 GLN H 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088410 restraints weight = 16968.857| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.90 r_work: 0.3149 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13286 Z= 0.224 Angle : 0.672 7.258 19249 Z= 0.398 Chirality : 0.039 0.157 2192 Planarity : 0.005 0.052 1372 Dihedral : 31.425 161.620 4208 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.78 % Allowed : 13.73 % Favored : 83.49 % 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: 1.48 (0.28), residues: 758 helix: 1.64 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 39 PHE 0.011 0.002 PHE E 67 TYR 0.010 0.002 TYR E 41 ARG 0.005 0.001 ARG H 27 Details of bonding type rmsd hydrogen bonds : bond 0.05562 ( 806) hydrogen bonds : angle 3.00577 ( 1998) covalent geometry : bond 0.00491 (13286) covalent geometry : angle 0.67191 (19249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.028 Fit side-chains REVERT: C 15 LYS cc_start: 0.8520 (ttpp) cc_final: 0.7939 (ttmm) REVERT: E 129 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8509 (tpt90) REVERT: G 72 ASP cc_start: 0.7889 (m-30) cc_final: 0.7673 (m-30) REVERT: G 104 GLN cc_start: 0.8754 (mt0) cc_final: 0.8504 (mm110) REVERT: H 29 THR cc_start: 0.7864 (t) cc_final: 0.7512 (p) outliers start: 18 outliers final: 1 residues processed: 188 average time/residue: 2.2503 time to fit residues: 444.3162 Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081151 restraints weight = 16781.754| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.92 r_work: 0.3008 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13286 Z= 0.295 Angle : 0.659 7.715 19249 Z= 0.389 Chirality : 0.040 0.164 2192 Planarity : 0.005 0.045 1372 Dihedral : 31.722 166.365 4202 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.39 % Allowed : 14.51 % Favored : 84.10 % 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: 2.02 (0.28), residues: 758 helix: 2.02 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 39 PHE 0.014 0.002 PHE E 67 TYR 0.013 0.002 TYR F 51 ARG 0.007 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 806) hydrogen bonds : angle 3.00506 ( 1998) covalent geometry : bond 0.00659 (13286) covalent geometry : angle 0.65934 (19249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.980 Fit side-chains REVERT: C 15 LYS cc_start: 0.8550 (ttpp) cc_final: 0.7952 (ttmm) REVERT: E 94 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: E 129 ARG cc_start: 0.8634 (tpt90) cc_final: 0.8378 (tpt90) REVERT: G 74 LYS cc_start: 0.8669 (mppt) cc_final: 0.8443 (mptt) REVERT: H 29 THR cc_start: 0.7993 (t) cc_final: 0.7652 (p) REVERT: H 90 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8237 (mp0) outliers start: 9 outliers final: 5 residues processed: 155 average time/residue: 2.5941 time to fit residues: 422.0247 Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082438 restraints weight = 16684.265| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.86 r_work: 0.3042 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13286 Z= 0.187 Angle : 0.601 7.733 19249 Z= 0.363 Chirality : 0.036 0.128 2192 Planarity : 0.005 0.053 1372 Dihedral : 31.710 166.916 4202 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.54 % Allowed : 14.97 % Favored : 83.49 % 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 (0.29), residues: 758 helix: 2.29 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.35 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 39 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.005 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 806) hydrogen bonds : angle 2.87615 ( 1998) covalent geometry : bond 0.00409 (13286) covalent geometry : angle 0.60060 (19249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.868 Fit side-chains REVERT: C 15 LYS cc_start: 0.8512 (ttpp) cc_final: 0.7904 (ttmm) REVERT: E 129 ARG cc_start: 0.8650 (tpt90) cc_final: 0.8445 (tpt90) REVERT: G 73 ASN cc_start: 0.8094 (t0) cc_final: 0.7869 (t160) REVERT: H 29 THR cc_start: 0.7988 (t) cc_final: 0.7702 (p) REVERT: H 90 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8194 (mp0) outliers start: 10 outliers final: 5 residues processed: 160 average time/residue: 2.2778 time to fit residues: 381.8747 Evaluate side-chains 155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083224 restraints weight = 16958.841| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.87 r_work: 0.3050 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.197 Angle : 0.581 6.972 19249 Z= 0.350 Chirality : 0.035 0.126 2192 Planarity : 0.005 0.050 1372 Dihedral : 31.254 167.814 4202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.23 % Allowed : 15.43 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.29), residues: 758 helix: 2.48 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 806) hydrogen bonds : angle 2.75891 ( 1998) covalent geometry : bond 0.00436 (13286) covalent geometry : angle 0.58133 (19249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 1.045 Fit side-chains REVERT: C 15 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7855 (ttmm) REVERT: E 94 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: E 129 ARG cc_start: 0.8634 (tpt90) cc_final: 0.8432 (tpt90) REVERT: G 73 ASN cc_start: 0.8208 (t0) cc_final: 0.7895 (t160) REVERT: H 29 THR cc_start: 0.8013 (t) cc_final: 0.7624 (p) REVERT: H 90 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8154 (mp0) outliers start: 8 outliers final: 2 residues processed: 155 average time/residue: 2.5510 time to fit residues: 415.7624 Evaluate side-chains 156 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083266 restraints weight = 16868.476| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.87 r_work: 0.3048 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.197 Angle : 0.582 6.788 19249 Z= 0.350 Chirality : 0.035 0.126 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.259 169.177 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.54 % Allowed : 15.28 % Favored : 83.18 % 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: 2.71 (0.29), residues: 758 helix: 2.52 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 806) hydrogen bonds : angle 2.76093 ( 1998) covalent geometry : bond 0.00434 (13286) covalent geometry : angle 0.58249 (19249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.990 Fit side-chains REVERT: C 15 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7791 (ttmm) REVERT: D 90 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: E 94 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: G 73 ASN cc_start: 0.8215 (t0) cc_final: 0.7847 (t160) REVERT: H 90 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8165 (mp0) outliers start: 10 outliers final: 6 residues processed: 158 average time/residue: 2.2485 time to fit residues: 372.7749 Evaluate side-chains 161 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083410 restraints weight = 16738.984| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 0.87 r_work: 0.3057 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13286 Z= 0.200 Angle : 0.586 6.691 19249 Z= 0.351 Chirality : 0.035 0.126 2192 Planarity : 0.005 0.048 1372 Dihedral : 31.245 169.844 4202 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.70 % Allowed : 14.97 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.29), residues: 758 helix: 2.50 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 806) hydrogen bonds : angle 2.75324 ( 1998) covalent geometry : bond 0.00443 (13286) covalent geometry : angle 0.58574 (19249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.918 Fit side-chains REVERT: C 15 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7787 (ttmm) REVERT: D 56 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8765 (tpp) REVERT: D 90 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: E 94 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: G 73 ASN cc_start: 0.8205 (t0) cc_final: 0.7800 (t160) REVERT: H 90 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8164 (mp0) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 2.3323 time to fit residues: 381.9143 Evaluate side-chains 159 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083236 restraints weight = 16851.990| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.87 r_work: 0.3047 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13286 Z= 0.203 Angle : 0.588 6.538 19249 Z= 0.353 Chirality : 0.035 0.148 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.244 170.222 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.85 % Allowed : 15.12 % Favored : 83.02 % 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: 2.77 (0.29), residues: 758 helix: 2.59 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 806) hydrogen bonds : angle 2.75999 ( 1998) covalent geometry : bond 0.00449 (13286) covalent geometry : angle 0.58752 (19249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.976 Fit side-chains REVERT: C 15 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7790 (ttmm) REVERT: D 56 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8761 (tpp) REVERT: G 73 ASN cc_start: 0.8204 (t0) cc_final: 0.7799 (t160) REVERT: H 90 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8176 (mp0) outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 2.1741 time to fit residues: 344.0900 Evaluate side-chains 154 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083312 restraints weight = 16702.219| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.86 r_work: 0.3049 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13286 Z= 0.197 Angle : 0.586 6.376 19249 Z= 0.352 Chirality : 0.035 0.138 2192 Planarity : 0.005 0.048 1372 Dihedral : 31.245 170.216 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.70 % Allowed : 15.59 % Favored : 82.72 % 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: 2.78 (0.29), residues: 758 helix: 2.60 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.27 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 806) hydrogen bonds : angle 2.76047 ( 1998) covalent geometry : bond 0.00436 (13286) covalent geometry : angle 0.58589 (19249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.903 Fit side-chains REVERT: C 15 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7786 (ttmm) REVERT: D 56 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8759 (tpp) REVERT: G 73 ASN cc_start: 0.8203 (t0) cc_final: 0.7789 (t160) REVERT: H 90 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8169 (mp0) outliers start: 11 outliers final: 9 residues processed: 148 average time/residue: 2.0733 time to fit residues: 322.4386 Evaluate side-chains 152 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083245 restraints weight = 16771.489| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.87 r_work: 0.3052 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13286 Z= 0.197 Angle : 0.586 6.574 19249 Z= 0.352 Chirality : 0.035 0.139 2192 Planarity : 0.005 0.050 1372 Dihedral : 31.240 170.254 4202 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.70 % Allowed : 15.74 % Favored : 82.56 % 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: 2.79 (0.29), residues: 758 helix: 2.60 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.24 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 806) hydrogen bonds : angle 2.76359 ( 1998) covalent geometry : bond 0.00437 (13286) covalent geometry : angle 0.58556 (19249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.994 Fit side-chains REVERT: C 15 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7781 (ttmm) REVERT: D 56 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8763 (tpp) REVERT: G 73 ASN cc_start: 0.8205 (t0) cc_final: 0.7783 (t160) REVERT: H 90 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8172 (mp0) outliers start: 11 outliers final: 10 residues processed: 148 average time/residue: 2.6551 time to fit residues: 413.0474 Evaluate side-chains 156 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083855 restraints weight = 16752.281| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 0.88 r_work: 0.3061 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13286 Z= 0.185 Angle : 0.579 6.723 19249 Z= 0.348 Chirality : 0.034 0.137 2192 Planarity : 0.005 0.048 1372 Dihedral : 31.204 170.269 4202 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.70 % Allowed : 15.90 % Favored : 82.41 % 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: 2.83 (0.29), residues: 758 helix: 2.62 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 806) hydrogen bonds : angle 2.74005 ( 1998) covalent geometry : bond 0.00409 (13286) covalent geometry : angle 0.57867 (19249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13069.88 seconds wall clock time: 231 minutes 2.57 seconds (13862.57 seconds total)