Starting phenix.real_space_refine on Tue Feb 3 22:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4o_37267/02_2026/8w4o_37267.map" } resolution = 3.23 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= -0.001 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 36 5.21 5 S 10 5.16 5 C 4356 2.51 5 N 763 2.21 5 O 878 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6046 Number of models: 1 Model: "" Number of chains: 6 Chain: "5" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1280 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 156} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "7" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1222 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 154} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "6" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1209 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 51 Chain: "5" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 914 Unusual residues: {'A86': 3, 'CLA': 11, 'ET4': 1, 'LHG': 3, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-4': 5, 'CLA:plan-5': 7, 'CLA:plan-3': 2} Unresolved non-hydrogen planarities: 58 Chain: "7" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 707 Unusual residues: {'A86': 2, 'CLA': 12, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-4': 7, 'CLA:plan-5': 10, 'CLA:plan-2': 1, 'CLA:plan-3': 4} Unresolved non-hydrogen planarities: 84 Chain: "6" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 714 Unusual residues: {'A86': 1, 'CLA': 13, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-5': 11, 'CLA:plan-4': 6, 'CLA:plan-3': 3} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 1.31, per 1000 atoms: 0.22 Number of scatterers: 6046 At special positions: 0 Unit cell: (80.56, 113.42, 66.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 3 15.00 Mg 36 11.99 O 878 8.00 N 763 7.00 C 4356 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 170.9 milliseconds 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 57.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain '5' and resid 61 through 95 removed outlier: 3.589A pdb=" N SER 5 66 " --> pdb=" O PRO 5 62 " (cutoff:3.500A) Proline residue: 5 89 - end of helix Processing helix chain '5' and resid 108 through 112 removed outlier: 3.570A pdb=" N VAL 5 112 " --> pdb=" O ALA 5 109 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 138 removed outlier: 3.819A pdb=" N LEU 5 120 " --> pdb=" O ASP 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 158 through 189 Processing helix chain '5' and resid 192 through 199 Processing helix chain '5' and resid 200 through 202 No H-bonds generated for 'chain '5' and resid 200 through 202' Processing helix chain '7' and resid 46 through 71 Processing helix chain '7' and resid 72 through 76 Processing helix chain '7' and resid 103 through 119 removed outlier: 3.638A pdb=" N LEU 7 113 " --> pdb=" O GLN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 126 through 130 Processing helix chain '7' and resid 139 through 168 removed outlier: 3.649A pdb=" N LEU 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 185 Processing helix chain '6' and resid 59 through 86 Processing helix chain '6' and resid 87 through 89 No H-bonds generated for 'chain '6' and resid 87 through 89' Processing helix chain '6' and resid 116 through 132 Processing helix chain '6' and resid 139 through 143 Processing helix chain '6' and resid 149 through 181 Processing helix chain '6' and resid 194 through 198 213 hydrogen bonds defined for protein. 606 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 1498 1.35 - 1.54: 4642 1.54 - 1.72: 152 1.72 - 1.91: 17 1.91 - 2.09: 144 Bond restraints: 6453 Sorted by residual: bond pdb=" C30 DD6 6 204 " pdb=" C31 DD6 6 204 " ideal model delta sigma weight residual 1.421 1.242 0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 1.418 1.242 0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C30 DD6 7 304 " pdb=" C31 DD6 7 304 " ideal model delta sigma weight residual 1.421 1.252 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C27 DD6 7 304 " pdb=" C29 DD6 7 304 " ideal model delta sigma weight residual 1.418 1.253 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C30 DD6 6 203 " pdb=" C31 DD6 6 203 " ideal model delta sigma weight residual 1.421 1.259 0.162 2.00e-02 2.50e+03 6.52e+01 ... (remaining 6448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.88: 9243 5.88 - 11.76: 169 11.76 - 17.63: 13 17.63 - 23.51: 0 23.51 - 29.39: 5 Bond angle restraints: 9430 Sorted by residual: angle pdb=" C14 A86 7 302 " pdb=" C15 A86 7 302 " pdb=" O1 A86 7 302 " ideal model delta sigma weight residual 115.67 86.28 29.39 3.00e+00 1.11e-01 9.60e+01 angle pdb=" C14 A86 7 301 " pdb=" C15 A86 7 301 " pdb=" O1 A86 7 301 " ideal model delta sigma weight residual 115.67 88.91 26.76 3.00e+00 1.11e-01 7.96e+01 angle pdb=" C14 A86 5 320 " pdb=" C15 A86 5 320 " pdb=" O1 A86 5 320 " ideal model delta sigma weight residual 115.67 89.12 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" C14 A86 6 202 " pdb=" C15 A86 6 202 " pdb=" O1 A86 6 202 " ideal model delta sigma weight residual 115.67 90.63 25.04 3.00e+00 1.11e-01 6.97e+01 angle pdb=" C14 A86 5 301 " pdb=" C15 A86 5 301 " pdb=" C20 A86 5 301 " ideal model delta sigma weight residual 117.95 93.30 24.65 3.00e+00 1.11e-01 6.75e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 2753 35.43 - 70.87: 225 70.87 - 106.30: 72 106.30 - 141.74: 32 141.74 - 177.17: 14 Dihedral angle restraints: 3096 sinusoidal: 1697 harmonic: 1399 Sorted by residual: dihedral pdb=" C34 A86 5 303 " pdb=" C38 A86 5 303 " pdb=" O4 A86 5 303 " pdb=" C39 A86 5 303 " ideal model delta sinusoidal sigma weight residual -177.27 -0.10 -177.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 ET4 5 302 " pdb=" C23 ET4 5 302 " pdb=" C32 ET4 5 302 " pdb=" C33 ET4 5 302 " ideal model delta sinusoidal sigma weight residual 170.20 -16.65 -173.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 7 302 " pdb=" C38 A86 7 302 " pdb=" O4 A86 7 302 " pdb=" C39 A86 7 302 " ideal model delta sinusoidal sigma weight residual -177.27 -6.51 -170.76 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 747 0.275 - 0.550: 12 0.550 - 0.825: 1 0.825 - 1.100: 2 1.100 - 1.375: 1 Chirality restraints: 763 Sorted by residual: chirality pdb=" C15 A86 5 301 " pdb=" C14 A86 5 301 " pdb=" C16 A86 5 301 " pdb=" C20 A86 5 301 " both_signs ideal model delta sigma weight residual True 1.20 2.58 -1.37 2.00e-01 2.50e+01 4.73e+01 chirality pdb=" C20 A86 5 303 " pdb=" C15 A86 5 303 " pdb=" C19 A86 5 303 " pdb=" C21 A86 5 303 " both_signs ideal model delta sigma weight residual True 1.08 0.12 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" C15 A86 5 303 " pdb=" C14 A86 5 303 " pdb=" C16 A86 5 303 " pdb=" C20 A86 5 303 " both_signs ideal model delta sigma weight residual True 1.20 0.35 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 760 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG 5 317 " 0.099 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C8 LHG 5 317 " -0.029 2.00e-02 2.50e+03 pdb=" O7 LHG 5 317 " -0.031 2.00e-02 2.50e+03 pdb=" O9 LHG 5 317 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG 5 318 " 0.082 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C24 LHG 5 318 " -0.025 2.00e-02 2.50e+03 pdb=" O10 LHG 5 318 " -0.030 2.00e-02 2.50e+03 pdb=" O8 LHG 5 318 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 SQD 5 319 " -0.076 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C24 SQD 5 319 " 0.023 2.00e-02 2.50e+03 pdb=" O10 SQD 5 319 " 0.029 2.00e-02 2.50e+03 pdb=" O48 SQD 5 319 " 0.024 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 905 2.77 - 3.30: 5388 3.30 - 3.83: 10499 3.83 - 4.37: 11702 4.37 - 4.90: 19387 Nonbonded interactions: 47881 Sorted by model distance: nonbonded pdb=" O ASP 5 199 " pdb=" OG SER 5 200 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU 6 70 " pdb=" NE ARG 6 162 " model vdw 2.268 3.120 nonbonded pdb=" OD2 ASP 7 37 " pdb=" OG SER 7 42 " model vdw 2.277 3.040 nonbonded pdb=" O ALA 5 125 " pdb=" OG SER 5 128 " model vdw 2.302 3.040 nonbonded pdb=" O PHE 6 184 " pdb=" O4 SQD 5 319 " model vdw 2.305 3.040 ... (remaining 47876 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 12.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.500 Find NCS groups from input model: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.040 0.887 6475 Z= 2.038 Angle : 1.697 29.389 9430 Z= 0.623 Chirality : 0.099 1.375 763 Planarity : 0.007 0.091 1276 Dihedral : 31.536 177.169 2206 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.85 % Favored : 85.95 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.38), residues: 491 helix: 0.31 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -4.38 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 6 133 TYR 0.010 0.001 TYR 6 84 PHE 0.013 0.001 PHE 6 136 TRP 0.009 0.001 TRP 6 92 HIS 0.004 0.001 HIS 7 60 Details of bonding type rmsd covalent geometry : bond 0.01138 ( 6453) covalent geometry : angle 1.69666 ( 9430) hydrogen bonds : bond 0.11881 ( 213) hydrogen bonds : angle 5.06091 ( 606) Misc. bond : bond 0.65316 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.173 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.0560 time to fit residues: 7.0266 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 80 GLN 7 109 GLN 7 164 GLN 6 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066432 restraints weight = 13750.623| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.91 r_work: 0.2665 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.046 2.304 6475 Z= 4.385 Angle : 0.849 11.503 9430 Z= 0.339 Chirality : 0.082 0.977 763 Planarity : 0.006 0.071 1276 Dihedral : 30.355 178.765 1439 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.15 % Favored : 91.45 % Rotamer: Outliers : 1.73 % Allowed : 12.14 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.39), residues: 491 helix: 1.23 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.51 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 91 TYR 0.010 0.001 TYR 7 77 PHE 0.010 0.001 PHE 6 125 TRP 0.012 0.001 TRP 6 135 HIS 0.004 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6453) covalent geometry : angle 0.84949 ( 9430) hydrogen bonds : bond 0.05754 ( 213) hydrogen bonds : angle 3.71430 ( 606) Misc. bond : bond 0.78702 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: 7 139 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: 6 107 ASN cc_start: 0.8673 (t0) cc_final: 0.8247 (t0) REVERT: 6 168 ILE cc_start: 0.9291 (tp) cc_final: 0.9051 (tp) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.0605 time to fit residues: 7.1391 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.0040 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.0040 chunk 11 optimal weight: 8.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3033 r_free = 0.3033 target = 0.078529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.067185 restraints weight = 13581.073| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.92 r_work: 0.2677 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.490 6475 Z= 0.154 Angle : 0.767 12.047 9430 Z= 0.313 Chirality : 0.077 0.906 763 Planarity : 0.005 0.058 1276 Dihedral : 29.131 174.252 1439 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 3.18 % Allowed : 12.72 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.39), residues: 491 helix: 1.63 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.25 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 91 TYR 0.011 0.001 TYR 5 94 PHE 0.008 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6453) covalent geometry : angle 0.76744 ( 9430) hydrogen bonds : bond 0.05480 ( 213) hydrogen bonds : angle 3.54297 ( 606) Misc. bond : bond 0.19443 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: 7 139 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: 6 84 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8300 (t80) REVERT: 6 107 ASN cc_start: 0.8680 (t0) cc_final: 0.8252 (t0) REVERT: 6 168 ILE cc_start: 0.9242 (tp) cc_final: 0.8944 (tp) REVERT: 6 175 ASP cc_start: 0.8725 (t0) cc_final: 0.8358 (t0) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.0608 time to fit residues: 6.5090 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 196 ASN ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 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 = 0.3020 r_free = 0.3020 target = 0.077741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066423 restraints weight = 13542.289| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.90 r_work: 0.2671 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.474 6475 Z= 0.164 Angle : 0.758 12.035 9430 Z= 0.312 Chirality : 0.076 0.910 763 Planarity : 0.005 0.052 1276 Dihedral : 28.692 170.872 1439 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.18 % Allowed : 13.87 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.38 (0.39), residues: 491 helix: 1.86 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.16 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 91 TYR 0.015 0.001 TYR 5 94 PHE 0.009 0.001 PHE 6 125 TRP 0.006 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6453) covalent geometry : angle 0.75790 ( 9430) hydrogen bonds : bond 0.05436 ( 213) hydrogen bonds : angle 3.49181 ( 606) Misc. bond : bond 0.18960 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.136 Fit side-chains REVERT: 6 84 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8403 (t80) REVERT: 6 107 ASN cc_start: 0.8684 (t0) cc_final: 0.8330 (t0) REVERT: 6 168 ILE cc_start: 0.9258 (tp) cc_final: 0.8945 (tp) REVERT: 6 175 ASP cc_start: 0.8735 (t0) cc_final: 0.8317 (t0) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.0584 time to fit residues: 6.3690 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.0030 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 196 ASN ** 7 109 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 = 0.3036 r_free = 0.3036 target = 0.078698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.067176 restraints weight = 13688.885| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.94 r_work: 0.2675 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.477 6475 Z= 0.142 Angle : 0.747 11.961 9430 Z= 0.309 Chirality : 0.076 0.918 763 Planarity : 0.005 0.048 1276 Dihedral : 28.522 168.887 1439 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 3.18 % Allowed : 15.03 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.26 (0.40), residues: 491 helix: 1.97 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.11 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 91 TYR 0.012 0.001 TYR 5 94 PHE 0.008 0.001 PHE 6 125 TRP 0.006 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6453) covalent geometry : angle 0.74656 ( 9430) hydrogen bonds : bond 0.05401 ( 213) hydrogen bonds : angle 3.45890 ( 606) Misc. bond : bond 0.18921 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8420 (t80) REVERT: 6 107 ASN cc_start: 0.8680 (t0) cc_final: 0.8341 (t0) REVERT: 6 168 ILE cc_start: 0.9254 (tp) cc_final: 0.8946 (tp) REVERT: 6 175 ASP cc_start: 0.8778 (t0) cc_final: 0.8375 (t0) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.0658 time to fit residues: 7.1656 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3012 r_free = 0.3012 target = 0.077245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.065868 restraints weight = 13677.387| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.91 r_work: 0.2659 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.458 6475 Z= 0.220 Angle : 0.784 12.032 9430 Z= 0.326 Chirality : 0.077 0.902 763 Planarity : 0.005 0.045 1276 Dihedral : 28.421 167.674 1439 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.85 % Rotamer: Outliers : 3.18 % Allowed : 15.90 % Favored : 80.92 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.33 % 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: -0.29 (0.39), residues: 491 helix: 1.93 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 91 TYR 0.012 0.001 TYR 5 94 PHE 0.009 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.005 0.002 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 6453) covalent geometry : angle 0.78397 ( 9430) hydrogen bonds : bond 0.05426 ( 213) hydrogen bonds : angle 3.58058 ( 606) Misc. bond : bond 0.18775 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8438 (t80) REVERT: 6 107 ASN cc_start: 0.8696 (t0) cc_final: 0.8360 (t0) REVERT: 6 168 ILE cc_start: 0.9272 (tp) cc_final: 0.8953 (tp) REVERT: 6 175 ASP cc_start: 0.8796 (t0) cc_final: 0.8390 (t0) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0644 time to fit residues: 6.9104 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3010 r_free = 0.3010 target = 0.077105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.065747 restraints weight = 13660.799| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.90 r_work: 0.2658 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.059 6475 Z= 1.335 Angle : 0.784 12.032 9430 Z= 0.326 Chirality : 0.077 0.902 763 Planarity : 0.005 0.045 1276 Dihedral : 28.479 167.674 1439 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.85 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % Favored : 80.64 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.33 % 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: -0.29 (0.39), residues: 491 helix: 1.93 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 91 TYR 0.012 0.001 TYR 5 94 PHE 0.009 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.005 0.002 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 6453) covalent geometry : angle 0.78405 ( 9430) hydrogen bonds : bond 0.05425 ( 213) hydrogen bonds : angle 3.58060 ( 606) Misc. bond : bond 0.29368 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8441 (t80) REVERT: 6 107 ASN cc_start: 0.8695 (t0) cc_final: 0.8360 (t0) REVERT: 6 168 ILE cc_start: 0.9269 (tp) cc_final: 0.8950 (tp) REVERT: 6 175 ASP cc_start: 0.8791 (t0) cc_final: 0.8384 (t0) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.0583 time to fit residues: 6.1743 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3009 r_free = 0.3009 target = 0.077095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065709 restraints weight = 13681.120| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.90 r_work: 0.2658 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.053 6475 Z= 1.327 Angle : 0.784 12.032 9430 Z= 0.326 Chirality : 0.077 0.902 763 Planarity : 0.005 0.045 1276 Dihedral : 28.478 167.673 1439 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.85 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % Favored : 80.64 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 3.33 % 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: -0.29 (0.39), residues: 491 helix: 1.93 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 6 91 TYR 0.012 0.001 TYR 5 94 PHE 0.009 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.005 0.002 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 6453) covalent geometry : angle 0.78413 ( 9430) hydrogen bonds : bond 0.05425 ( 213) hydrogen bonds : angle 3.58061 ( 606) Misc. bond : bond 0.29262 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8440 (t80) REVERT: 6 107 ASN cc_start: 0.8695 (t0) cc_final: 0.8361 (t0) REVERT: 6 168 ILE cc_start: 0.9269 (tp) cc_final: 0.8951 (tp) REVERT: 6 175 ASP cc_start: 0.8793 (t0) cc_final: 0.8386 (t0) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.0640 time to fit residues: 6.6901 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 17 optimal weight: 0.0970 chunk 37 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.067512 restraints weight = 13638.528| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.92 r_work: 0.2682 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 2.359 6475 Z= 2.934 Angle : 0.786 16.497 9430 Z= 0.332 Chirality : 0.078 0.929 763 Planarity : 0.005 0.051 1276 Dihedral : 28.223 165.016 1439 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.74 % Favored : 92.06 % Rotamer: Outliers : 2.60 % Allowed : 17.34 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.39), residues: 491 helix: 1.97 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.04 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 91 TYR 0.017 0.001 TYR 5 94 PHE 0.008 0.001 PHE 6 125 TRP 0.005 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6453) covalent geometry : angle 0.78564 ( 9430) hydrogen bonds : bond 0.05342 ( 213) hydrogen bonds : angle 3.55125 ( 606) Misc. bond : bond 0.53710 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9266 (OUTLIER) cc_final: 0.8465 (t80) REVERT: 6 107 ASN cc_start: 0.8691 (t0) cc_final: 0.8369 (t0) REVERT: 6 168 ILE cc_start: 0.9241 (tp) cc_final: 0.8921 (tp) REVERT: 6 175 ASP cc_start: 0.8749 (t0) cc_final: 0.8324 (t0) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.0607 time to fit residues: 6.6222 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 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 = 0.3026 r_free = 0.3026 target = 0.078006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.066496 restraints weight = 13681.768| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.92 r_work: 0.2670 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.449 6475 Z= 0.207 Angle : 0.833 14.249 9430 Z= 0.367 Chirality : 0.077 0.916 763 Planarity : 0.006 0.077 1276 Dihedral : 28.008 161.358 1439 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 2.60 % Allowed : 17.63 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.39), residues: 491 helix: 2.02 (0.31), residues: 266 sheet: None (None), residues: 0 loop : -3.05 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 6 91 TYR 0.021 0.001 TYR 5 94 PHE 0.011 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.005 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6453) covalent geometry : angle 0.83290 ( 9430) hydrogen bonds : bond 0.05530 ( 213) hydrogen bonds : angle 3.74358 ( 606) Misc. bond : bond 0.18518 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8518 (t80) REVERT: 6 107 ASN cc_start: 0.8683 (t0) cc_final: 0.8372 (t0) REVERT: 6 168 ILE cc_start: 0.9248 (tp) cc_final: 0.8920 (tp) REVERT: 6 175 ASP cc_start: 0.8795 (t0) cc_final: 0.8389 (t0) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0604 time to fit residues: 6.1719 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 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 = 0.3016 r_free = 0.3016 target = 0.077370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066007 restraints weight = 13704.341| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.92 r_work: 0.2668 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.449 6475 Z= 0.200 Angle : 0.824 14.074 9430 Z= 0.360 Chirality : 0.077 0.916 763 Planarity : 0.006 0.057 1276 Dihedral : 27.938 161.318 1439 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 2.31 % Allowed : 19.08 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.18 (0.39), residues: 491 helix: 2.03 (0.30), residues: 266 sheet: None (None), residues: 0 loop : -3.04 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 91 TYR 0.017 0.001 TYR 5 94 PHE 0.011 0.001 PHE 6 125 TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6453) covalent geometry : angle 0.82391 ( 9430) hydrogen bonds : bond 0.05510 ( 213) hydrogen bonds : angle 3.73300 ( 606) Misc. bond : bond 0.18521 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.93 seconds wall clock time: 29 minutes 39.82 seconds (1779.82 seconds total)