Starting phenix.real_space_refine on Fri Jul 25 10:24:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_37267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_37267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_37267.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_37267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4o_37267/07_2025/8w4o_37267.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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-3': 2, 'CLA:plan-4': 5, 'CLA:plan-5': 7} 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-2': 1, 'CLA:plan-3': 4, 'CLA:plan-4': 7, 'CLA:plan-5': 10} 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-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 6.91, per 1000 atoms: 1.14 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: 3.09 Conformation dependent library (CDL) restraints added in 529.4 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: 0.39 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: 1.38 Time building geometry restraints manager: 3.01 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: 8.500 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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 : 20.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (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 TRP 0.009 0.001 TRP 6 92 HIS 0.004 0.001 HIS 7 60 PHE 0.013 0.001 PHE 6 136 TYR 0.010 0.001 TYR 6 84 ARG 0.003 0.001 ARG 6 133 Details of bonding type rmsd hydrogen bonds : bond 0.11881 ( 213) hydrogen bonds : angle 5.06091 ( 606) covalent geometry : bond 0.01138 ( 6453) covalent geometry : angle 1.69666 ( 9430) 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 : 0.514 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.1421 time to fit residues: 17.2613 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 : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 80 GLN ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 164 GLN 6 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.077438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.066272 restraints weight = 13542.521| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.87 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: 0.8573 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.038 2.321 6475 Z= 3.607 Angle : 0.885 12.075 9430 Z= 0.354 Chirality : 0.080 0.921 763 Planarity : 0.006 0.075 1276 Dihedral : 31.384 178.050 1439 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.76 % Favored : 90.84 % Rotamer: Outliers : 2.60 % Allowed : 11.56 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.38), residues: 491 helix: 1.07 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.59 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 135 HIS 0.005 0.001 HIS 5 75 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 7 77 ARG 0.004 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.06106 ( 213) hydrogen bonds : angle 3.84901 ( 606) covalent geometry : bond 0.00439 ( 6453) covalent geometry : angle 0.88505 ( 9430) Misc. bond : bond 0.65177 ( 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.7935 (t80) REVERT: 6 91 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8298 (mtt90) REVERT: 6 107 ASN cc_start: 0.8689 (t0) cc_final: 0.8264 (t0) REVERT: 6 175 ASP cc_start: 0.8710 (t0) cc_final: 0.8314 (t0) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.1412 time to fit residues: 16.4221 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL 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 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 33 optimal weight: 0.0270 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 44 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 198 GLN ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3033 r_free = 0.3033 target = 0.078494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.067037 restraints weight = 13573.630| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.92 r_work: 0.2677 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.506 6475 Z= 0.157 Angle : 0.851 11.871 9430 Z= 0.343 Chirality : 0.079 0.923 763 Planarity : 0.006 0.068 1276 Dihedral : 30.960 176.522 1439 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.57 % Favored : 90.22 % Rotamer: Outliers : 3.18 % Allowed : 12.43 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.39), residues: 491 helix: 1.36 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.46 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.007 0.001 PHE 6 63 TYR 0.013 0.001 TYR 7 77 ARG 0.003 0.000 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 213) hydrogen bonds : angle 3.67666 ( 606) covalent geometry : bond 0.00298 ( 6453) covalent geometry : angle 0.85127 ( 9430) Misc. bond : bond 0.20546 ( 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 : 0.535 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8095 (t80) REVERT: 6 107 ASN cc_start: 0.8680 (t0) cc_final: 0.8312 (t0) REVERT: 6 168 ILE cc_start: 0.9235 (tp) cc_final: 0.8967 (tp) REVERT: 6 175 ASP cc_start: 0.8707 (t0) cc_final: 0.8302 (t0) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.1275 time to fit residues: 13.7919 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 68 VAL Chi-restraints excluded: chain 7 residue 91 ASP 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 109 VAL 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 9 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 109 GLN ** 6 122 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 = 0.3018 r_free = 0.3018 target = 0.077623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.066109 restraints weight = 13773.467| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.92 r_work: 0.2655 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 2.040 6475 Z= 2.542 Angle : 0.804 12.207 9430 Z= 0.322 Chirality : 0.077 0.904 763 Planarity : 0.005 0.059 1276 Dihedral : 29.651 178.078 1439 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.96 % Favored : 90.84 % Rotamer: Outliers : 2.02 % Allowed : 14.16 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.39), residues: 491 helix: 1.65 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.29 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.017 0.001 TYR 5 94 ARG 0.006 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05850 ( 213) hydrogen bonds : angle 3.64518 ( 606) covalent geometry : bond 0.00379 ( 6453) covalent geometry : angle 0.80360 ( 9430) Misc. bond : bond 0.47828 ( 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: 7 poor density : 73 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: 7 164 GLN cc_start: 0.7097 (mt0) cc_final: 0.6881 (mt0) REVERT: 6 84 TYR cc_start: 0.9320 (OUTLIER) cc_final: 0.8244 (t80) REVERT: 6 107 ASN cc_start: 0.8720 (t0) cc_final: 0.8287 (t0) REVERT: 6 168 ILE cc_start: 0.9259 (tp) cc_final: 0.8967 (tp) REVERT: 6 175 ASP cc_start: 0.8774 (t0) cc_final: 0.8369 (t0) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.1269 time to fit residues: 13.8644 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL 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 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 29 optimal weight: 0.0870 overall best weight: 0.2536 ------------------------------------------------------------------------------- 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** ** 7 164 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 = 0.3034 r_free = 0.3034 target = 0.078592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.067052 restraints weight = 13526.826| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.93 r_work: 0.2674 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.340 6475 Z= 0.226 Angle : 0.798 12.082 9430 Z= 0.329 Chirality : 0.078 0.913 763 Planarity : 0.006 0.055 1276 Dihedral : 29.293 170.842 1439 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 2.89 % Allowed : 13.29 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.39), residues: 491 helix: 1.80 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.19 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.007 0.001 PHE 6 94 TYR 0.013 0.001 TYR 5 94 ARG 0.007 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05634 ( 213) hydrogen bonds : angle 3.50190 ( 606) covalent geometry : bond 0.00294 ( 6453) covalent geometry : angle 0.79809 ( 9430) Misc. bond : bond 0.34516 ( 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 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8334 (t80) REVERT: 6 107 ASN cc_start: 0.8682 (t0) cc_final: 0.8286 (t0) REVERT: 6 168 ILE cc_start: 0.9252 (tp) cc_final: 0.8947 (tp) REVERT: 6 175 ASP cc_start: 0.8731 (t0) cc_final: 0.8270 (t0) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1332 time to fit residues: 14.7091 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 : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3027 r_free = 0.3027 target = 0.078256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.066804 restraints weight = 13519.022| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.92 r_work: 0.2669 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.483 6475 Z= 0.249 Angle : 0.777 12.112 9430 Z= 0.316 Chirality : 0.076 0.903 763 Planarity : 0.005 0.051 1276 Dihedral : 29.078 169.572 1439 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.55 % Favored : 91.24 % Rotamer: Outliers : 2.60 % Allowed : 15.03 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.39), residues: 491 helix: 1.79 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.15 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.012 0.001 TYR 5 94 ARG 0.008 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05553 ( 213) hydrogen bonds : angle 3.55355 ( 606) covalent geometry : bond 0.00339 ( 6453) covalent geometry : angle 0.77706 ( 9430) Misc. bond : bond 0.37033 ( 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.463 Fit side-chains REVERT: 6 84 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8361 (t80) REVERT: 6 107 ASN cc_start: 0.8688 (t0) cc_final: 0.8298 (t0) REVERT: 6 168 ILE cc_start: 0.9259 (tp) cc_final: 0.8960 (tp) REVERT: 6 175 ASP cc_start: 0.8771 (t0) cc_final: 0.8353 (t0) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.1273 time to fit residues: 13.3653 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.2318 ------------------------------------------------------------------------------- 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** ** 6 122 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 = 0.3038 r_free = 0.3038 target = 0.078817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067339 restraints weight = 13468.038| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.92 r_work: 0.2679 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.336 6475 Z= 0.220 Angle : 0.758 12.038 9430 Z= 0.310 Chirality : 0.077 0.913 763 Planarity : 0.005 0.048 1276 Dihedral : 28.753 167.366 1439 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.16 % Favored : 90.63 % Rotamer: Outliers : 3.18 % Allowed : 16.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.39), residues: 491 helix: 1.89 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.09 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.014 0.001 TYR 5 94 ARG 0.008 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 213) hydrogen bonds : angle 3.56807 ( 606) covalent geometry : bond 0.00277 ( 6453) covalent geometry : angle 0.75787 ( 9430) Misc. bond : bond 0.34390 ( 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 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9249 (OUTLIER) cc_final: 0.8376 (t80) REVERT: 6 107 ASN cc_start: 0.8674 (t0) cc_final: 0.8375 (t0) REVERT: 6 168 ILE cc_start: 0.9249 (tp) cc_final: 0.8933 (tp) REVERT: 6 175 ASP cc_start: 0.8748 (t0) cc_final: 0.8288 (t0) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.1567 time to fit residues: 18.1166 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 : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL 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 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3009 r_free = 0.3009 target = 0.077111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.065702 restraints weight = 13594.237| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.90 r_work: 0.2656 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.018 1.098 6475 Z= 0.248 Angle : 0.820 12.153 9430 Z= 0.346 Chirality : 0.077 0.909 763 Planarity : 0.006 0.047 1276 Dihedral : 28.410 163.748 1439 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 2.89 % Allowed : 16.76 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.39), residues: 491 helix: 2.00 (0.30), residues: 266 sheet: None (None), residues: 0 loop : -3.03 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.005 0.002 HIS 6 73 PHE 0.012 0.001 PHE 6 125 TYR 0.019 0.001 TYR 5 94 ARG 0.009 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 213) hydrogen bonds : angle 3.79631 ( 606) covalent geometry : bond 0.00431 ( 6453) covalent geometry : angle 0.82016 ( 9430) Misc. bond : bond 0.29940 ( 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 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8418 (t80) REVERT: 6 107 ASN cc_start: 0.8708 (t0) cc_final: 0.8336 (t0) REVERT: 6 168 ILE cc_start: 0.9265 (tp) cc_final: 0.8935 (tp) REVERT: 6 175 ASP cc_start: 0.8767 (t0) cc_final: 0.8318 (t0) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.1599 time to fit residues: 17.4337 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 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 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.077556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066104 restraints weight = 13524.308| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.92 r_work: 0.2662 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.073 6475 Z= 0.213 Angle : 0.788 11.960 9430 Z= 0.334 Chirality : 0.077 0.918 763 Planarity : 0.005 0.047 1276 Dihedral : 28.329 163.229 1439 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.85 % Rotamer: Outliers : 2.02 % Allowed : 18.79 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.39), residues: 491 helix: 2.03 (0.31), residues: 266 sheet: None (None), residues: 0 loop : -3.00 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.010 0.001 PHE 6 125 TYR 0.016 0.001 TYR 5 94 ARG 0.009 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05630 ( 213) hydrogen bonds : angle 3.70037 ( 606) covalent geometry : bond 0.00340 ( 6453) covalent geometry : angle 0.78754 ( 9430) Misc. bond : bond 0.29492 ( 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9273 (OUTLIER) cc_final: 0.8493 (t80) REVERT: 6 107 ASN cc_start: 0.8704 (t0) cc_final: 0.8347 (t0) REVERT: 6 168 ILE cc_start: 0.9253 (tp) cc_final: 0.8923 (tp) REVERT: 6 175 ASP cc_start: 0.8753 (t0) cc_final: 0.8297 (t0) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.1497 time to fit residues: 16.1776 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL 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 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.2254 ------------------------------------------------------------------------------- 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** 6 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.067238 restraints weight = 13620.225| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.94 r_work: 0.2680 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 2.361 6475 Z= 2.940 Angle : 0.792 16.655 9430 Z= 0.338 Chirality : 0.077 0.924 763 Planarity : 0.005 0.046 1276 Dihedral : 28.071 161.521 1439 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.85 % Rotamer: Outliers : 1.73 % Allowed : 18.79 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.39), residues: 491 helix: 1.97 (0.30), residues: 268 sheet: None (None), residues: 0 loop : -2.90 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.015 0.001 TYR 5 94 ARG 0.009 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 213) hydrogen bonds : angle 3.61497 ( 606) covalent geometry : bond 0.00290 ( 6453) covalent geometry : angle 0.79182 ( 9430) Misc. bond : bond 0.57900 ( 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 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8489 (t80) REVERT: 6 107 ASN cc_start: 0.8699 (t0) cc_final: 0.8352 (t0) REVERT: 6 168 ILE cc_start: 0.9238 (tp) cc_final: 0.8912 (tp) REVERT: 6 175 ASP cc_start: 0.8732 (t0) cc_final: 0.8229 (t0) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.1226 time to fit residues: 12.8966 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 VAL 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 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3025 r_free = 0.3025 target = 0.077899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.066550 restraints weight = 13851.687| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.93 r_work: 0.2675 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.017 0.991 6475 Z= 0.253 Angle : 0.852 16.955 9430 Z= 0.380 Chirality : 0.077 0.910 763 Planarity : 0.006 0.101 1276 Dihedral : 27.992 160.806 1439 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % Rotamer: Outliers : 2.02 % Allowed : 18.79 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.39), residues: 491 helix: 1.96 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -2.89 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 92 HIS 0.004 0.001 HIS 5 75 PHE 0.008 0.001 PHE 6 125 TYR 0.009 0.001 TYR 7 77 ARG 0.009 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 213) hydrogen bonds : angle 3.66819 ( 606) covalent geometry : bond 0.00450 ( 6453) covalent geometry : angle 0.85177 ( 9430) Misc. bond : bond 0.28286 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3707.09 seconds wall clock time: 65 minutes 30.22 seconds (3930.22 seconds total)