Starting phenix.real_space_refine on Sat May 2 16:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzp_49955/05_2026/9nzp_49955.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 199 5.49 5 S 14 5.16 5 C 3929 2.51 5 N 1327 2.21 5 O 1928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7397 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1596 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 2, 'TRANS': 192} Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1588 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 2, 'TRANS': 191} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3399 Classifications: {'RNA': 159} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 77, 'rna3p_pyr': 58} Link IDs: {'rna2p': 24, 'rna3p': 134} Time building chain proxies: 1.84, per 1000 atoms: 0.25 Number of scatterers: 7397 At special positions: 0 Unit cell: (101.26, 87.98, 128.65, 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 14 16.00 P 199 15.00 O 1928 8.00 N 1327 7.00 C 3929 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: 0.85 Conformation dependent library (CDL) restraints added in 263.5 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 44.2% alpha, 19.8% beta 56 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 removed outlier: 4.005A pdb=" N SER A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.500A pdb=" N PHE A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.824A pdb=" N SER A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'B' and resid 15 through 46 removed outlier: 3.655A pdb=" N ALA B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.710A pdb=" N LYS B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 147 through 152 removed outlier: 4.605A pdb=" N TYR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 3.559A pdb=" N ARG B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.620A pdb=" N LEU A 114 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 176 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 185 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.620A pdb=" N LEU A 114 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 176 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 171 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.552A pdb=" N SER B 176 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.552A pdb=" N SER B 176 " --> pdb=" O ASN B 188 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1478 1.34 - 1.46: 2885 1.46 - 1.58: 3166 1.58 - 1.70: 395 1.70 - 1.82: 24 Bond restraints: 7948 Sorted by residual: bond pdb=" C3' U E 9 " pdb=" O3' U E 9 " ideal model delta sigma weight residual 1.427 1.458 -0.031 1.50e-02 4.44e+03 4.30e+00 bond pdb=" CB GLU B 169 " pdb=" CG GLU B 169 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" CB ASN B 17 " pdb=" CG ASN B 17 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.31e+00 bond pdb=" CB GLU A 51 " pdb=" CG GLU A 51 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.04e+00 bond pdb=" C3' U E 55 " pdb=" C2' U E 55 " ideal model delta sigma weight residual 1.525 1.550 -0.025 1.50e-02 4.44e+03 2.67e+00 ... (remaining 7943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 10975 2.12 - 4.24: 560 4.24 - 6.36: 81 6.36 - 8.48: 30 8.48 - 10.60: 9 Bond angle restraints: 11655 Sorted by residual: angle pdb=" C4' U E 9 " pdb=" C3' U E 9 " pdb=" O3' U E 9 " ideal model delta sigma weight residual 109.40 116.75 -7.35 1.50e+00 4.44e-01 2.40e+01 angle pdb=" C3' U E 9 " pdb=" O3' U E 9 " pdb=" P U E 10 " ideal model delta sigma weight residual 120.20 127.20 -7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C3' G E 135 " pdb=" O3' G E 135 " pdb=" P U E 136 " ideal model delta sigma weight residual 120.20 127.06 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' A E 138 " pdb=" P A E 139 " pdb=" O5' A E 139 " ideal model delta sigma weight residual 104.00 110.83 -6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" O3' G E 135 " pdb=" P U E 136 " pdb=" O5' U E 136 " ideal model delta sigma weight residual 104.00 110.67 -6.67 1.50e+00 4.44e-01 1.98e+01 ... (remaining 11650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 4148 34.74 - 69.47: 637 69.47 - 104.21: 65 104.21 - 138.95: 5 138.95 - 173.68: 9 Dihedral angle restraints: 4864 sinusoidal: 3715 harmonic: 1149 Sorted by residual: dihedral pdb=" O4' U E 53 " pdb=" C1' U E 53 " pdb=" N1 U E 53 " pdb=" C2 U E 53 " ideal model delta sinusoidal sigma weight residual 200.00 50.66 149.34 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' C E 110 " pdb=" C1' C E 110 " pdb=" N1 C E 110 " pdb=" C2 C E 110 " ideal model delta sinusoidal sigma weight residual 232.00 58.32 173.68 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U E 106 " pdb=" C1' U E 106 " pdb=" N1 U E 106 " pdb=" C2 U E 106 " ideal model delta sinusoidal sigma weight residual 232.00 61.16 170.84 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 4861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1132 0.060 - 0.121: 236 0.121 - 0.181: 44 0.181 - 0.242: 14 0.242 - 0.302: 6 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' U E 9 " pdb=" C4' U E 9 " pdb=" O3' U E 9 " pdb=" C2' U E 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C4' U E 136 " pdb=" C5' U E 136 " pdb=" O4' U E 136 " pdb=" C3' U E 136 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P G E 49 " pdb=" OP1 G E 49 " pdb=" OP2 G E 49 " pdb=" O5' G E 49 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1429 not shown) Planarity restraints: 745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 2 " 0.030 2.00e-02 2.50e+03 3.05e-02 2.09e+01 pdb=" N1 C E 2 " -0.074 2.00e-02 2.50e+03 pdb=" C2 C E 2 " 0.041 2.00e-02 2.50e+03 pdb=" O2 C E 2 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C E 2 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C E 2 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C E 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C E 2 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C E 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 38 " 0.043 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A E 38 " -0.057 2.00e-02 2.50e+03 pdb=" C8 A E 38 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A E 38 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A E 38 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 38 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A E 38 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A E 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 38 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A E 38 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A E 38 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 53 " 0.046 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 U E 53 " -0.051 2.00e-02 2.50e+03 pdb=" C2 U E 53 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U E 53 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U E 53 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U E 53 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U E 53 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U E 53 " -0.014 2.00e-02 2.50e+03 ... (remaining 742 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2668 2.90 - 3.40: 6478 3.40 - 3.90: 14648 3.90 - 4.40: 15866 4.40 - 4.90: 21804 Nonbonded interactions: 61464 Sorted by model distance: nonbonded pdb=" N4 DC C 11 " pdb=" N6 A E 159 " model vdw 2.401 2.560 nonbonded pdb=" O5' A E 8 " pdb=" O4' A E 8 " model vdw 2.468 2.432 nonbonded pdb=" O5' A E 52 " pdb=" O4' A E 52 " model vdw 2.480 2.432 nonbonded pdb=" O5' C E 92 " pdb=" O4' C E 92 " model vdw 2.482 2.432 nonbonded pdb=" O5' A E 100 " pdb=" O4' A E 100 " model vdw 2.488 2.432 ... (remaining 61459 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' and resid 1 through 194) selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 2.230 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7948 Z= 0.291 Angle : 1.117 10.596 11655 Z= 0.611 Chirality : 0.056 0.302 1432 Planarity : 0.007 0.049 745 Dihedral : 26.656 173.682 4122 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.28 % Allowed : 33.61 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.42), residues: 385 helix: 1.60 (0.41), residues: 153 sheet: -1.08 (0.59), residues: 71 loop : -0.94 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 24 TYR 0.025 0.003 TYR B 45 PHE 0.014 0.002 PHE A 179 TRP 0.010 0.003 TRP B 137 HIS 0.006 0.002 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 7948) covalent geometry : angle 1.11675 (11655) hydrogen bonds : bond 0.12761 ( 304) hydrogen bonds : angle 5.68195 ( 749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0957 time to fit residues: 13.5590 Evaluate side-chains 71 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 139 ASN B 154 ASN B 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.100877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.073806 restraints weight = 28077.598| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.80 r_work: 0.3259 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7948 Z= 0.221 Angle : 0.767 8.307 11655 Z= 0.388 Chirality : 0.040 0.272 1432 Planarity : 0.004 0.025 745 Dihedral : 26.149 178.017 3300 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.60 % Allowed : 32.21 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.43), residues: 385 helix: 1.81 (0.42), residues: 152 sheet: -0.66 (0.61), residues: 73 loop : -0.69 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 16 TYR 0.017 0.002 TYR B 45 PHE 0.018 0.002 PHE B 161 TRP 0.002 0.001 TRP A 137 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 7948) covalent geometry : angle 0.76658 (11655) hydrogen bonds : bond 0.06157 ( 304) hydrogen bonds : angle 3.98282 ( 749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8962 (mp0) cc_final: 0.8539 (mp0) REVERT: A 187 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7922 (tp) REVERT: B 18 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (pm20) REVERT: B 51 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8838 (tm-30) REVERT: B 122 LYS cc_start: 0.7913 (tppt) cc_final: 0.7707 (tppt) outliers start: 20 outliers final: 7 residues processed: 75 average time/residue: 0.0828 time to fit residues: 8.5607 Evaluate side-chains 60 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.097455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.069074 restraints weight = 27296.393| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.75 r_work: 0.3201 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7948 Z= 0.240 Angle : 0.731 11.043 11655 Z= 0.372 Chirality : 0.040 0.264 1432 Planarity : 0.004 0.025 745 Dihedral : 26.021 175.615 3300 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.48 % Allowed : 31.09 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.42), residues: 385 helix: 1.58 (0.40), residues: 153 sheet: -0.61 (0.63), residues: 74 loop : -0.86 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 106 TYR 0.019 0.002 TYR A 125 PHE 0.012 0.002 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.004 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7948) covalent geometry : angle 0.73101 (11655) hydrogen bonds : bond 0.05981 ( 304) hydrogen bonds : angle 3.90122 ( 749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7057 (mmm) cc_final: 0.6835 (tpt) REVERT: A 18 GLU cc_start: 0.8914 (mp0) cc_final: 0.8485 (mp0) REVERT: A 71 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8666 (t0) REVERT: A 102 GLU cc_start: 0.8617 (mp0) cc_final: 0.8137 (mt-10) REVERT: A 109 LYS cc_start: 0.8713 (mmtp) cc_final: 0.8461 (mmtm) REVERT: A 169 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8568 (tm-30) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.0801 time to fit residues: 7.2292 Evaluate side-chains 56 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.100787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072862 restraints weight = 27535.753| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.83 r_work: 0.3245 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7948 Z= 0.136 Angle : 0.599 8.329 11655 Z= 0.306 Chirality : 0.034 0.246 1432 Planarity : 0.003 0.025 745 Dihedral : 25.771 175.454 3300 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.64 % Allowed : 34.17 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.43), residues: 385 helix: 1.99 (0.41), residues: 154 sheet: -0.62 (0.63), residues: 74 loop : -0.87 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 103 TYR 0.015 0.002 TYR A 125 PHE 0.011 0.001 PHE B 161 TRP 0.004 0.001 TRP B 137 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7948) covalent geometry : angle 0.59905 (11655) hydrogen bonds : bond 0.05046 ( 304) hydrogen bonds : angle 3.37707 ( 749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6911 (mmm) cc_final: 0.6707 (tpt) REVERT: A 18 GLU cc_start: 0.9085 (mp0) cc_final: 0.8662 (mp0) REVERT: A 102 GLU cc_start: 0.8485 (mp0) cc_final: 0.8103 (mt-10) REVERT: A 109 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8403 (mmtm) REVERT: A 169 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8644 (tm-30) REVERT: B 55 GLU cc_start: 0.9047 (tp30) cc_final: 0.8811 (mm-30) REVERT: B 100 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8683 (ttpp) REVERT: B 174 GLN cc_start: 0.8892 (tt0) cc_final: 0.8640 (tt0) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.0713 time to fit residues: 6.2534 Evaluate side-chains 54 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.095930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067624 restraints weight = 27818.709| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.81 r_work: 0.3148 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7948 Z= 0.213 Angle : 0.663 7.860 11655 Z= 0.342 Chirality : 0.037 0.262 1432 Planarity : 0.004 0.024 745 Dihedral : 25.818 178.551 3300 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.44 % Allowed : 29.97 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.44), residues: 385 helix: 2.20 (0.42), residues: 155 sheet: -0.48 (0.71), residues: 59 loop : -0.75 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.020 0.002 TYR A 125 PHE 0.012 0.001 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7948) covalent geometry : angle 0.66325 (11655) hydrogen bonds : bond 0.05657 ( 304) hydrogen bonds : angle 3.58900 ( 749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7087 (mmm) cc_final: 0.6849 (tpt) REVERT: A 18 GLU cc_start: 0.9040 (mp0) cc_final: 0.8606 (mp0) REVERT: A 70 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8722 (mt) REVERT: A 102 GLU cc_start: 0.8658 (mp0) cc_final: 0.8300 (mt-10) REVERT: A 109 LYS cc_start: 0.8725 (mmtp) cc_final: 0.8393 (mmtm) REVERT: A 169 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 18 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: B 48 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8921 (mtm-85) REVERT: B 100 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8797 (ttpt) outliers start: 23 outliers final: 12 residues processed: 71 average time/residue: 0.0808 time to fit residues: 7.8883 Evaluate side-chains 62 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 175 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 54 optimal weight: 10.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.096861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069086 restraints weight = 27369.655| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.77 r_work: 0.3185 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.8777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7948 Z= 0.178 Angle : 0.613 6.821 11655 Z= 0.318 Chirality : 0.035 0.253 1432 Planarity : 0.003 0.024 745 Dihedral : 25.724 175.412 3300 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.16 % Allowed : 28.29 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.44), residues: 385 helix: 2.12 (0.41), residues: 155 sheet: -0.46 (0.72), residues: 59 loop : -0.76 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.020 0.002 TYR B 20 PHE 0.014 0.001 PHE B 161 TRP 0.004 0.001 TRP B 137 HIS 0.001 0.000 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7948) covalent geometry : angle 0.61317 (11655) hydrogen bonds : bond 0.05250 ( 304) hydrogen bonds : angle 3.49559 ( 749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.183 Fit side-chains REVERT: A 1 MET cc_start: 0.7016 (mmm) cc_final: 0.6808 (tpt) REVERT: A 5 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8029 (mmm-85) REVERT: A 18 GLU cc_start: 0.9068 (mp0) cc_final: 0.8636 (mp0) REVERT: A 70 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 71 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 102 GLU cc_start: 0.8568 (mp0) cc_final: 0.8233 (mt-10) REVERT: A 109 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8422 (mmtm) REVERT: A 169 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 6 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7310 (mttp) REVERT: B 18 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8802 (pm20) REVERT: B 100 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8673 (ttpp) REVERT: B 189 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7045 (tt) outliers start: 22 outliers final: 11 residues processed: 69 average time/residue: 0.0833 time to fit residues: 7.8872 Evaluate side-chains 62 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.093838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065701 restraints weight = 27873.371| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.74 r_work: 0.3134 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.9381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7948 Z= 0.229 Angle : 0.663 6.894 11655 Z= 0.347 Chirality : 0.038 0.265 1432 Planarity : 0.004 0.023 745 Dihedral : 25.937 178.210 3300 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 7.00 % Allowed : 26.61 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.45), residues: 385 helix: 2.16 (0.42), residues: 155 sheet: -0.73 (0.69), residues: 69 loop : -0.74 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.027 0.003 TYR B 20 PHE 0.015 0.002 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 7948) covalent geometry : angle 0.66312 (11655) hydrogen bonds : bond 0.05855 ( 304) hydrogen bonds : angle 3.57257 ( 749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7320 (mmm) cc_final: 0.7112 (tpt) REVERT: A 18 GLU cc_start: 0.9066 (mp0) cc_final: 0.8633 (mp0) REVERT: A 71 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8648 (t0) REVERT: A 102 GLU cc_start: 0.8696 (mp0) cc_final: 0.8310 (mt-10) REVERT: B 6 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7653 (mttp) REVERT: B 18 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8714 (pm20) REVERT: B 100 LYS cc_start: 0.9142 (ttpt) cc_final: 0.8688 (ttpp) REVERT: B 189 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7327 (tt) outliers start: 25 outliers final: 12 residues processed: 69 average time/residue: 0.0774 time to fit residues: 7.4460 Evaluate side-chains 62 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.098930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.071371 restraints weight = 27830.889| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.76 r_work: 0.3253 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.9454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7948 Z= 0.126 Angle : 0.578 7.168 11655 Z= 0.303 Chirality : 0.034 0.240 1432 Planarity : 0.003 0.028 745 Dihedral : 25.691 178.588 3300 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.48 % Allowed : 28.57 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.44), residues: 385 helix: 2.12 (0.41), residues: 155 sheet: -0.58 (0.70), residues: 61 loop : -0.74 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.019 0.002 TYR A 125 PHE 0.014 0.001 PHE B 161 TRP 0.007 0.001 TRP B 137 HIS 0.001 0.000 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7948) covalent geometry : angle 0.57772 (11655) hydrogen bonds : bond 0.05116 ( 304) hydrogen bonds : angle 3.20763 ( 749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8124 (mmm-85) REVERT: A 18 GLU cc_start: 0.9105 (mp0) cc_final: 0.8705 (mp0) REVERT: B 6 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7521 (mttp) REVERT: B 18 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8709 (pm20) REVERT: B 100 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8953 (ttpp) REVERT: B 174 GLN cc_start: 0.8768 (tt0) cc_final: 0.8516 (tt0) REVERT: B 189 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7085 (tt) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.0800 time to fit residues: 7.1571 Evaluate side-chains 61 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.098276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.070734 restraints weight = 27605.016| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.72 r_work: 0.3243 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.9585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7948 Z= 0.132 Angle : 0.571 9.318 11655 Z= 0.297 Chirality : 0.034 0.249 1432 Planarity : 0.003 0.029 745 Dihedral : 25.636 177.474 3300 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.92 % Allowed : 29.41 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.45), residues: 385 helix: 2.28 (0.41), residues: 155 sheet: -0.49 (0.68), residues: 64 loop : -0.66 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.026 0.002 TYR B 20 PHE 0.021 0.001 PHE B 161 TRP 0.004 0.001 TRP B 137 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7948) covalent geometry : angle 0.57108 (11655) hydrogen bonds : bond 0.05080 ( 304) hydrogen bonds : angle 3.16292 ( 749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.9087 (mp0) cc_final: 0.8664 (mp0) REVERT: A 102 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 6 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7737 (mttp) REVERT: B 18 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8693 (pm20) REVERT: B 20 TYR cc_start: 0.9163 (m-80) cc_final: 0.8770 (m-10) REVERT: B 100 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8743 (ttpp) REVERT: B 189 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7065 (tt) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.0819 time to fit residues: 6.8911 Evaluate side-chains 60 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.098196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.070900 restraints weight = 27438.828| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.69 r_work: 0.3239 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.9701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7948 Z= 0.137 Angle : 0.581 10.687 11655 Z= 0.300 Chirality : 0.034 0.251 1432 Planarity : 0.003 0.027 745 Dihedral : 25.606 179.482 3300 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.36 % Allowed : 29.13 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.45), residues: 385 helix: 2.30 (0.41), residues: 155 sheet: -0.25 (0.70), residues: 64 loop : -0.71 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.025 0.002 TYR B 20 PHE 0.023 0.001 PHE B 161 TRP 0.005 0.001 TRP B 137 HIS 0.002 0.000 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7948) covalent geometry : angle 0.58109 (11655) hydrogen bonds : bond 0.05065 ( 304) hydrogen bonds : angle 3.19090 ( 749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7494 (tpt) cc_final: 0.7143 (tpt) REVERT: A 18 GLU cc_start: 0.9090 (mp0) cc_final: 0.8663 (mp0) REVERT: A 102 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 6 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7774 (mttp) REVERT: B 18 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8681 (pm20) REVERT: B 20 TYR cc_start: 0.9145 (m-80) cc_final: 0.8714 (m-10) REVERT: B 189 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7109 (tt) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.0767 time to fit residues: 6.4717 Evaluate side-chains 60 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.098611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071407 restraints weight = 27271.430| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.70 r_work: 0.3250 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.9770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7948 Z= 0.132 Angle : 0.580 12.622 11655 Z= 0.298 Chirality : 0.033 0.250 1432 Planarity : 0.003 0.028 745 Dihedral : 25.565 178.227 3300 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.64 % Allowed : 29.13 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.44), residues: 385 helix: 2.26 (0.41), residues: 155 sheet: -0.09 (0.69), residues: 64 loop : -0.74 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.023 0.002 TYR B 20 PHE 0.023 0.001 PHE B 161 TRP 0.005 0.001 TRP B 137 HIS 0.001 0.000 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7948) covalent geometry : angle 0.58011 (11655) hydrogen bonds : bond 0.05041 ( 304) hydrogen bonds : angle 3.13693 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.87 seconds wall clock time: 35 minutes 38.31 seconds (2138.31 seconds total)