Starting phenix.real_space_refine on Thu Mar 13 05:10:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.map" model { file = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhy_11221/03_2025/6zhy_11221.cif" } resolution = 3.0 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= 0.002 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 218 5.49 5 S 8 5.16 5 C 4968 2.51 5 N 1700 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2236 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2268 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 5.68, per 1000 atoms: 0.63 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.758, 107.256, 101.37, 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 8 16.00 P 218 15.00 O 2105 8.00 N 1700 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 535.1 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 73.5% alpha, 2.5% beta 110 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.097A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.860A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.853A 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 132 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 removed outlier: 3.787A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.400A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 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 100 through 121 removed outlier: 3.588A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.818A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.915A 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 131 Processing helix chain 'F' and resid 24 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 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.663A 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 42 through 43 removed outlier: 7.157A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.620A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.472A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 306 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1561 1.33 - 1.45: 3291 1.45 - 1.57: 4300 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9605 Sorted by residual: bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.67e+00 bond pdb=" C3' DG J -19 " pdb=" C2' DG J -19 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 12009 1.20 - 2.40: 1415 2.40 - 3.60: 382 3.60 - 4.80: 81 4.80 - 6.00: 20 Bond angle restraints: 13907 Sorted by residual: angle pdb=" O3' DT J -17 " pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 111.50 117.50 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C4' DT I 30 " pdb=" O4' DT I 30 " pdb=" C1' DT I 30 " ideal model delta sigma weight residual 109.70 103.81 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.97 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.40 102.78 5.62 1.50e+00 4.44e-01 1.41e+01 angle pdb=" O4' DG I 28 " pdb=" C1' DG I 28 " pdb=" N9 DG I 28 " ideal model delta sigma weight residual 108.40 102.99 5.41 1.50e+00 4.44e-01 1.30e+01 ... (remaining 13902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 4197 33.42 - 66.83: 967 66.83 - 100.25: 36 100.25 - 133.66: 0 133.66 - 167.07: 2 Dihedral angle restraints: 5202 sinusoidal: 3573 harmonic: 1629 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1285 0.068 - 0.136: 245 0.136 - 0.204: 25 0.204 - 0.273: 18 0.273 - 0.341: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C4' DT J 69 " pdb=" C5' DT J 69 " pdb=" O4' DT J 69 " pdb=" C3' DT J 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C4' DC I 4 " pdb=" C5' DC I 4 " pdb=" O4' DC I 4 " pdb=" C3' DC I 4 " both_signs ideal model delta sigma weight residual False -2.53 -2.22 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1576 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.063 2.00e-02 2.50e+03 3.45e-02 2.67e+01 pdb=" N1 DC I 6 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.053 2.00e-02 2.50e+03 3.09e-02 2.14e+01 pdb=" N1 DC I 4 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " -0.042 2.00e-02 2.50e+03 2.86e-02 1.84e+01 pdb=" N1 DC J 19 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " -0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2053 2.83 - 3.35: 8482 3.35 - 3.87: 18066 3.87 - 4.38: 21277 4.38 - 4.90: 29320 Nonbonded interactions: 79198 Sorted by model distance: nonbonded pdb=" OE1 GLN B 93 " pdb=" NH1 ARG B 95 " model vdw 2.316 3.120 nonbonded pdb=" NH2 ARG E 116 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.406 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.420 3.040 nonbonded pdb=" OE1 GLU D 68 " pdb=" NZ LYS F 91 " model vdw 2.427 3.120 ... (remaining 79193 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.930 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.005 0.082 9605 Z= 0.248 Angle : 0.911 5.999 13907 Z= 0.590 Chirality : 0.061 0.341 1579 Planarity : 0.014 0.138 999 Dihedral : 27.253 167.075 4150 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.21 % Allowed : 0.43 % Favored : 99.36 % 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: 0.65 (0.31), residues: 548 helix: 0.73 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE F 100 TYR 0.027 0.004 TYR C 57 ARG 0.030 0.004 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 90 ASP cc_start: 0.8348 (t70) cc_final: 0.8132 (t70) REVERT: F 31 LYS cc_start: 0.8916 (tttt) cc_final: 0.8648 (tttp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 1.6983 time to fit residues: 322.6222 Evaluate side-chains 123 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 73 ASN D 44 GLN D 46 HIS D 92 GLN E 39 HIS E 68 GLN E 85 GLN E 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.078949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053029 restraints weight = 23515.748| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.15 r_work: 0.2678 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9605 Z= 0.351 Angle : 0.669 5.565 13907 Z= 0.404 Chirality : 0.039 0.131 1579 Planarity : 0.005 0.044 999 Dihedral : 32.060 166.868 3019 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.48 % Allowed : 15.99 % Favored : 79.53 % 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: 2.54 (0.35), residues: 548 helix: 2.31 (0.25), residues: 399 sheet: None (None), residues: 0 loop : -0.04 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE F 61 TYR 0.010 0.002 TYR C 57 ARG 0.007 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8887 (tp30) cc_final: 0.8561 (tp30) REVERT: C 56 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: E 59 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: E 118 THR cc_start: 0.9459 (m) cc_final: 0.9245 (p) REVERT: F 31 LYS cc_start: 0.9133 (tttt) cc_final: 0.8879 (tttp) REVERT: F 63 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8472 (mt-10) outliers start: 21 outliers final: 9 residues processed: 145 average time/residue: 1.5833 time to fit residues: 241.1014 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS C 68 ASN D 44 GLN E 68 GLN E 108 ASN E 113 HIS E 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056391 restraints weight = 24313.975| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.08 r_work: 0.2771 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9605 Z= 0.188 Angle : 0.578 5.317 13907 Z= 0.355 Chirality : 0.035 0.129 1579 Planarity : 0.004 0.046 999 Dihedral : 31.238 174.453 3019 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.26 % Allowed : 19.40 % Favored : 76.33 % 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: 3.12 (0.35), residues: 548 helix: 2.75 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.06 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.011 0.001 PHE D 67 TYR 0.008 0.001 TYR C 57 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8737 (tp30) cc_final: 0.8503 (tp30) REVERT: C 56 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: D 90 GLU cc_start: 0.8640 (mp0) cc_final: 0.8003 (mp0) REVERT: E 120 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8500 (mtm) outliers start: 20 outliers final: 8 residues processed: 153 average time/residue: 1.3960 time to fit residues: 225.6294 Evaluate side-chains 137 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 68 ASN D 44 GLN D 46 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053814 restraints weight = 24036.110| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.11 r_work: 0.2695 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9605 Z= 0.293 Angle : 0.601 5.452 13907 Z= 0.360 Chirality : 0.035 0.132 1579 Planarity : 0.004 0.043 999 Dihedral : 31.510 178.963 3019 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 5.33 % Allowed : 20.04 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.36), residues: 548 helix: 2.87 (0.26), residues: 401 sheet: None (None), residues: 0 loop : 0.05 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 46 PHE 0.008 0.001 PHE E 67 TYR 0.008 0.001 TYR C 57 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8772 (mttm) REVERT: B 53 GLU cc_start: 0.8716 (tp30) cc_final: 0.8515 (tp30) REVERT: C 56 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: D 90 GLU cc_start: 0.8696 (mp0) cc_final: 0.8486 (mp0) REVERT: F 31 LYS cc_start: 0.9144 (tttt) cc_final: 0.8907 (tttp) outliers start: 25 outliers final: 10 residues processed: 140 average time/residue: 1.5146 time to fit residues: 222.9096 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.080982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055960 restraints weight = 23911.903| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.08 r_work: 0.2758 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9605 Z= 0.179 Angle : 0.570 5.614 13907 Z= 0.344 Chirality : 0.033 0.123 1579 Planarity : 0.004 0.045 999 Dihedral : 31.217 178.243 3019 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.84 % Allowed : 21.75 % Favored : 74.41 % 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: 3.44 (0.36), residues: 548 helix: 2.96 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.23 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.008 0.001 TYR D 80 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: D 90 GLU cc_start: 0.8637 (mp0) cc_final: 0.8418 (mp0) REVERT: D 102 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8195 (mm-30) outliers start: 18 outliers final: 8 residues processed: 141 average time/residue: 1.6812 time to fit residues: 249.9810 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.053534 restraints weight = 24044.026| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.08 r_work: 0.2688 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9605 Z= 0.326 Angle : 0.607 5.946 13907 Z= 0.361 Chirality : 0.035 0.131 1579 Planarity : 0.004 0.045 999 Dihedral : 31.384 175.049 3019 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.26 % Allowed : 22.60 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.36), residues: 548 helix: 2.88 (0.26), residues: 405 sheet: None (None), residues: 0 loop : 0.15 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.009 0.001 TYR D 39 ARG 0.011 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: E 59 GLU cc_start: 0.8744 (pm20) cc_final: 0.8088 (pm20) REVERT: F 31 LYS cc_start: 0.9123 (tttt) cc_final: 0.8890 (tttp) outliers start: 20 outliers final: 10 residues processed: 134 average time/residue: 1.5505 time to fit residues: 218.6789 Evaluate side-chains 130 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054965 restraints weight = 24203.909| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.10 r_work: 0.2736 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9605 Z= 0.194 Angle : 0.577 5.852 13907 Z= 0.347 Chirality : 0.033 0.125 1579 Planarity : 0.004 0.046 999 Dihedral : 31.213 173.319 3019 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.26 % Allowed : 23.67 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.36), residues: 548 helix: 2.91 (0.26), residues: 405 sheet: None (None), residues: 0 loop : 0.24 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.009 0.001 TYR F 51 ARG 0.010 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: E 59 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8391 (pm20) outliers start: 20 outliers final: 9 residues processed: 136 average time/residue: 1.4697 time to fit residues: 210.3871 Evaluate side-chains 135 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.052458 restraints weight = 24629.828| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.13 r_work: 0.2658 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 9605 Z= 0.406 Angle : 0.642 6.948 13907 Z= 0.378 Chirality : 0.037 0.131 1579 Planarity : 0.005 0.049 999 Dihedral : 31.464 169.745 3019 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.48 % Allowed : 24.31 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.37), residues: 548 helix: 2.79 (0.26), residues: 405 sheet: None (None), residues: 0 loop : 0.03 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.002 TYR D 80 ARG 0.009 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: D 90 GLU cc_start: 0.8636 (mp0) cc_final: 0.8425 (mp0) REVERT: E 59 GLU cc_start: 0.8812 (pm20) cc_final: 0.8165 (pm20) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 1.5378 time to fit residues: 214.7708 Evaluate side-chains 132 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055215 restraints weight = 24115.605| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.09 r_work: 0.2736 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9605 Z= 0.195 Angle : 0.591 7.155 13907 Z= 0.352 Chirality : 0.033 0.127 1579 Planarity : 0.004 0.043 999 Dihedral : 31.150 166.988 3019 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.77 % Allowed : 26.44 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.36), residues: 548 helix: 2.91 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.18 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR D 80 ARG 0.009 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: D 90 GLU cc_start: 0.8593 (mp0) cc_final: 0.8043 (mp0) REVERT: E 59 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8512 (pm20) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 1.5065 time to fit residues: 223.5168 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055374 restraints weight = 24319.306| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.09 r_work: 0.2741 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9605 Z= 0.215 Angle : 0.602 7.380 13907 Z= 0.355 Chirality : 0.033 0.125 1579 Planarity : 0.004 0.044 999 Dihedral : 31.047 165.899 3019 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.56 % Allowed : 26.23 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.36), residues: 548 helix: 2.95 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.20 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR D 80 ARG 0.010 0.000 ARG D 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: D 90 GLU cc_start: 0.8609 (mp0) cc_final: 0.8052 (mp0) REVERT: E 59 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8605 (pm20) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 1.6226 time to fit residues: 235.3245 Evaluate side-chains 137 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055542 restraints weight = 24109.301| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.07 r_work: 0.2745 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9605 Z= 0.213 Angle : 0.600 8.557 13907 Z= 0.353 Chirality : 0.033 0.125 1579 Planarity : 0.005 0.066 999 Dihedral : 31.032 165.560 3019 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.20 % Allowed : 26.23 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.36), residues: 548 helix: 2.94 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.23 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.025 0.001 TYR D 80 ARG 0.011 0.001 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6871.66 seconds wall clock time: 118 minutes 58.86 seconds (7138.86 seconds total)