Starting phenix.real_space_refine on Thu Feb 13 03:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhy_11221/02_2025/6zhy_11221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhy_11221/02_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_11221/02_2025/6zhy_11221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhy_11221/02_2025/6zhy_11221.map" model { file = "/net/cci-nas-00/data/ceres_data/6zhy_11221/02_2025/6zhy_11221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhy_11221/02_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-5592/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: 5.27, per 1000 atoms: 0.59 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: 2.28 Conformation dependent library (CDL) restraints added in 590.3 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: 4.51 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: 3.46 Time building geometry restraints manager: 2.64 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: 1.450 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.150 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- 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 : 0.719 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: 1.7708 time to fit residues: 336.3076 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 : 0.653 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053033 restraints weight = 23515.751| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.15 r_work: 0.2678 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 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 : 0.717 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8884 (tp30) cc_final: 0.8559 (tp30) REVERT: C 56 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: E 59 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: E 118 THR cc_start: 0.9460 (m) cc_final: 0.9246 (p) REVERT: F 31 LYS cc_start: 0.9135 (tttt) cc_final: 0.8882 (tttp) REVERT: F 63 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8468 (mt-10) outliers start: 21 outliers final: 9 residues processed: 145 average time/residue: 1.6248 time to fit residues: 247.5295 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 : 0.695 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 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: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.081626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.056925 restraints weight = 24408.822| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.09 r_work: 0.2789 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9605 Z= 0.182 Angle : 0.575 5.370 13907 Z= 0.353 Chirality : 0.034 0.130 1579 Planarity : 0.004 0.044 999 Dihedral : 31.128 175.658 3019 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.05 % Allowed : 19.19 % Favored : 76.76 % 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: 3.16 (0.35), residues: 548 helix: 2.78 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.07 (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 D 37 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 166 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9272 (mmm-85) cc_final: 0.9042 (mmm-85) REVERT: B 53 GLU cc_start: 0.8700 (tp30) cc_final: 0.8443 (tp30) REVERT: C 56 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: D 90 GLU cc_start: 0.8623 (mp0) cc_final: 0.8028 (mp0) outliers start: 19 outliers final: 6 residues processed: 152 average time/residue: 1.4392 time to fit residues: 230.8249 Evaluate side-chains 138 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 120 SER Chi-restraints excluded: chain E residue 80 THR 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: 0.9980 chunk 66 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 D 46 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.053453 restraints weight = 24048.291| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.07 r_work: 0.2688 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3289 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= 0.322 Angle : 0.611 5.723 13907 Z= 0.365 Chirality : 0.036 0.135 1579 Planarity : 0.004 0.044 999 Dihedral : 31.569 178.853 3019 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 5.12 % Allowed : 20.90 % Favored : 73.99 % 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: 3.21 (0.36), residues: 548 helix: 2.82 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.06 (0.49), residues: 144 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 B 51 ARG 0.007 0.001 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 150 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9112 (mp) REVERT: B 53 GLU cc_start: 0.8722 (tp30) cc_final: 0.8482 (tp30) REVERT: C 56 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: D 90 GLU cc_start: 0.8714 (mp0) cc_final: 0.8508 (mp0) REVERT: F 31 LYS cc_start: 0.9146 (tttt) cc_final: 0.8906 (tttp) outliers start: 24 outliers final: 12 residues processed: 138 average time/residue: 1.5605 time to fit residues: 226.2461 Evaluate side-chains 137 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN 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 = 0.3541 r_free = 0.3541 target = 0.080471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055401 restraints weight = 23945.214| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.08 r_work: 0.2745 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9605 Z= 0.203 Angle : 0.574 7.650 13907 Z= 0.345 Chirality : 0.033 0.122 1579 Planarity : 0.004 0.044 999 Dihedral : 31.192 177.182 3019 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.84 % Allowed : 22.60 % Favored : 73.56 % 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: 3.44 (0.36), residues: 548 helix: 2.96 (0.25), residues: 405 sheet: None (None), residues: 0 loop : 0.22 (0.50), residues: 143 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 0.007 0.001 TYR C 57 ARG 0.011 0.000 ARG B 35 *********************** 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 151 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (mttm) REVERT: C 56 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: D 90 GLU cc_start: 0.8678 (mp0) cc_final: 0.8452 (mp0) REVERT: E 120 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8680 (mtm) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 1.5001 time to fit residues: 221.0995 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 : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 SER 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=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: 0.7980 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.079178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053934 restraints weight = 24035.925| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.10 r_work: 0.2698 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3537 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= 0.304 Angle : 0.600 6.227 13907 Z= 0.358 Chirality : 0.035 0.131 1579 Planarity : 0.004 0.046 999 Dihedral : 31.301 174.742 3019 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.48 % Allowed : 21.96 % Favored : 73.56 % 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: 3.36 (0.36), residues: 548 helix: 2.91 (0.26), residues: 405 sheet: None (None), residues: 0 loop : 0.15 (0.50), 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 F 51 ARG 0.009 0.000 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 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8762 (mttm) REVERT: A 109 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 56 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: D 102 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 59 GLU cc_start: 0.8719 (pm20) cc_final: 0.8065 (pm20) REVERT: E 120 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8753 (mtm) outliers start: 21 outliers final: 9 residues processed: 134 average time/residue: 1.5468 time to fit residues: 218.0422 Evaluate side-chains 133 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 31 LYS 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 120 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET 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: 0.9980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 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 ** 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 = 0.3531 r_free = 0.3531 target = 0.080109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054941 restraints weight = 24090.045| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.09 r_work: 0.2731 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3598 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= 0.191 Angle : 0.580 8.073 13907 Z= 0.348 Chirality : 0.033 0.126 1579 Planarity : 0.004 0.045 999 Dihedral : 31.267 174.155 3019 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.05 % Allowed : 24.09 % Favored : 71.86 % 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: 3.35 (0.36), residues: 548 helix: 2.91 (0.26), residues: 404 sheet: None (None), residues: 0 loop : 0.16 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.008 0.001 PHE E 67 TYR 0.009 0.001 TYR D 80 ARG 0.008 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 149 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9067 (mp) REVERT: C 56 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: E 59 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: E 120 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (mtm) outliers start: 19 outliers final: 13 residues processed: 139 average time/residue: 1.5034 time to fit residues: 220.3525 Evaluate side-chains 143 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 31 LYS 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 44 GLN Chi-restraints excluded: chain D residue 58 ILE 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 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET 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: 0.0980 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: 0.8980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.079347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053924 restraints weight = 24577.947| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.11 r_work: 0.2699 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9605 Z= 0.298 Angle : 0.609 8.455 13907 Z= 0.361 Chirality : 0.034 0.127 1579 Planarity : 0.005 0.048 999 Dihedral : 31.233 170.571 3019 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.84 % Allowed : 24.52 % Favored : 71.64 % 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: 2.89 (0.26), residues: 405 sheet: None (None), residues: 0 loop : 0.12 (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 0.010 0.001 TYR D 80 ARG 0.010 0.000 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 144 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9087 (mp) REVERT: C 56 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: D 90 GLU cc_start: 0.8608 (mp0) cc_final: 0.8075 (mp0) REVERT: E 59 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: E 120 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8735 (mtm) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 1.5589 time to fit residues: 219.4526 Evaluate side-chains 136 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 31 LYS 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 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 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 = 0.3542 r_free = 0.3542 target = 0.080572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055473 restraints weight = 24100.872| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.09 r_work: 0.2740 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9605 Z= 0.189 Angle : 0.593 8.180 13907 Z= 0.352 Chirality : 0.033 0.128 1579 Planarity : 0.005 0.045 999 Dihedral : 31.190 169.989 3019 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.26 % Allowed : 25.37 % Favored : 70.36 % 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: 3.36 (0.36), residues: 548 helix: 2.91 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.20 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR D 80 ARG 0.010 0.001 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 150 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: D 90 GLU cc_start: 0.8555 (mp0) cc_final: 0.8045 (mp0) REVERT: D 102 GLU cc_start: 0.8427 (tp30) cc_final: 0.8220 (mm-30) REVERT: E 59 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (pm20) outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 1.4671 time to fit residues: 214.9974 Evaluate side-chains 143 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 31 LYS 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 44 GLN 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 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER 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: 6.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055457 restraints weight = 24321.353| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.08 r_work: 0.2743 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3799 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= 0.219 Angle : 0.603 8.023 13907 Z= 0.355 Chirality : 0.033 0.127 1579 Planarity : 0.004 0.045 999 Dihedral : 31.054 168.492 3019 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.41 % Allowed : 25.80 % 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: 3.43 (0.36), residues: 548 helix: 2.96 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.20 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.001 TYR D 80 ARG 0.010 0.001 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 146 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: D 90 GLU cc_start: 0.8581 (mp0) cc_final: 0.8048 (mp0) REVERT: E 59 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: F 25 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8558 (m110) outliers start: 16 outliers final: 8 residues processed: 137 average time/residue: 1.5200 time to fit residues: 219.1872 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 : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU 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 44 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 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: 4.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 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 = 0.3545 r_free = 0.3545 target = 0.080646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.055581 restraints weight = 24081.985| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.08 r_work: 0.2742 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9605 Z= 0.231 Angle : 0.875 59.193 13907 Z= 0.531 Chirality : 0.036 0.583 1579 Planarity : 0.004 0.045 999 Dihedral : 31.058 168.476 3019 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.82 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 25.80 % Favored : 71.22 % Cbeta Deviations : 0.19 % 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: 2.97 (0.25), residues: 404 sheet: None (None), residues: 0 loop : 0.21 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR D 80 ARG 0.009 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6418.62 seconds wall clock time: 113 minutes 35.92 seconds (6815.92 seconds total)