Starting phenix.real_space_refine on Wed Jul 23 20:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.map" model { file = "/net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irv_60822/07_2025/9irv_60822.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 2680 2.51 5 N 753 2.21 5 O 816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4258 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1215 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "B" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1215 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "C" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1358 Unusual residues: {'CRO': 1} Classifications: {'peptide': 165, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158, None: 1} Not linked: pdbres="CRO C 66 " pdbres="VAL C 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.86 Number of scatterers: 4258 At special positions: 0 Unit cell: (83.928, 101.144, 103.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 816 8.00 N 753 7.00 C 2680 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 478.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 43.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.736A pdb=" N ARG A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.609A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.606A pdb=" N VAL A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 198 through 216 Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.575A pdb=" N ALA B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.613A pdb=" N LEU B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.537A pdb=" N LEU B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.596A pdb=" N VAL B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 56 through 61 removed outlier: 4.111A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.643A pdb=" N SER C 72 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 5.120A pdb=" N ARG C 80 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 82 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.542A pdb=" N MET C 88 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 22 removed outlier: 6.374A pdb=" N ASN C 149 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS C 166 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 165 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 125 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 127 " --> pdb=" O ASP C 21 " (cutoff:3.500A) 226 hydrogen bonds defined for protein. 636 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: 1.09 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 762 1.29 - 1.42: 1047 1.42 - 1.55: 2514 1.55 - 1.68: 0 1.68 - 1.81: 14 Bond restraints: 4337 Sorted by residual: bond pdb=" C THR C 63 " pdb=" N LEU C 64 " ideal model delta sigma weight residual 1.329 1.246 0.083 1.40e-02 5.10e+03 3.52e+01 bond pdb=" C2 CRO C 66 " pdb=" N3 CRO C 66 " ideal model delta sigma weight residual 1.375 1.267 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CB2 CRO C 66 " pdb=" CA2 CRO C 66 " ideal model delta sigma weight residual 1.348 1.449 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" CA2 CRO C 66 " pdb=" N2 CRO C 66 " ideal model delta sigma weight residual 1.388 1.312 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C VAL C 68 " pdb=" O VAL C 68 " ideal model delta sigma weight residual 1.231 1.165 0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 4332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 5691 2.25 - 4.49: 171 4.49 - 6.74: 19 6.74 - 8.99: 6 8.99 - 11.24: 1 Bond angle restraints: 5888 Sorted by residual: angle pdb=" N GLY A 97 " pdb=" CA GLY A 97 " pdb=" C GLY A 97 " ideal model delta sigma weight residual 113.18 101.94 11.24 2.37e+00 1.78e-01 2.25e+01 angle pdb=" C THR C 63 " pdb=" N LEU C 64 " pdb=" CA LEU C 64 " ideal model delta sigma weight residual 121.70 129.33 -7.63 1.80e+00 3.09e-01 1.80e+01 angle pdb=" C VAL C 68 " pdb=" N GLN C 69 " pdb=" CA GLN C 69 " ideal model delta sigma weight residual 122.31 114.80 7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA VAL C 68 " pdb=" C VAL C 68 " pdb=" N GLN C 69 " ideal model delta sigma weight residual 116.20 108.79 7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" O VAL C 68 " pdb=" C VAL C 68 " pdb=" N GLN C 69 " ideal model delta sigma weight residual 123.00 128.12 -5.12 1.60e+00 3.91e-01 1.02e+01 ... (remaining 5883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2324 17.92 - 35.83: 188 35.83 - 53.75: 32 53.75 - 71.67: 11 71.67 - 89.59: 6 Dihedral angle restraints: 2561 sinusoidal: 984 harmonic: 1577 Sorted by residual: dihedral pdb=" CA GLY B 97 " pdb=" C GLY B 97 " pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N LEU B 99 " pdb=" CA LEU B 99 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLY A 97 " pdb=" C GLY A 97 " pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 366 0.037 - 0.074: 208 0.074 - 0.112: 70 0.112 - 0.149: 26 0.149 - 0.186: 2 Chirality restraints: 672 Sorted by residual: chirality pdb=" CA ILE C 123 " pdb=" N ILE C 123 " pdb=" C ILE C 123 " pdb=" CB ILE C 123 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ASN B 195 " pdb=" N ASN B 195 " pdb=" C ASN B 195 " pdb=" CB ASN B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 669 not shown) Planarity restraints: 777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO C 66 " -0.041 2.00e-02 2.50e+03 3.41e-02 2.90e+01 pdb=" CG2 CRO C 66 " 0.068 2.00e-02 2.50e+03 pdb=" C1 CRO C 66 " -0.033 2.00e-02 2.50e+03 pdb=" C2 CRO C 66 " -0.024 2.00e-02 2.50e+03 pdb=" CA1 CRO C 66 " 0.011 2.00e-02 2.50e+03 pdb=" CA2 CRO C 66 " -0.014 2.00e-02 2.50e+03 pdb=" CA3 CRO C 66 " 0.055 2.00e-02 2.50e+03 pdb=" N2 CRO C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N3 CRO C 66 " -0.005 2.00e-02 2.50e+03 pdb=" O2 CRO C 66 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB2 CRO C 66 " 0.014 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG2 CRO C 66 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 CRO C 66 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 CRO C 66 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 CRO C 66 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 CRO C 66 " 0.016 2.00e-02 2.50e+03 pdb=" CZ CRO C 66 " -0.006 2.00e-02 2.50e+03 pdb=" OH CRO C 66 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 63 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C THR C 63 " -0.055 2.00e-02 2.50e+03 pdb=" O THR C 63 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 64 " 0.019 2.00e-02 2.50e+03 ... (remaining 774 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 847 2.77 - 3.30: 3847 3.30 - 3.83: 6590 3.83 - 4.37: 7764 4.37 - 4.90: 13583 Nonbonded interactions: 32631 Sorted by model distance: nonbonded pdb=" OE1 GLU B 209 " pdb=" NH2 ARG B 212 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASP B 66 " pdb=" CD1 ILE B 101 " model vdw 2.264 3.460 nonbonded pdb=" OE1 GLU A 209 " pdb=" NH2 ARG A 212 " model vdw 2.272 3.120 nonbonded pdb=" N ASP A 83 " pdb=" OD1 ASP A 83 " model vdw 2.325 3.120 nonbonded pdb=" O LEU C 60 " pdb=" OG1 THR C 63 " model vdw 2.349 3.040 ... (remaining 32626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.008 0.162 4339 Z= 0.429 Angle : 0.924 11.236 5888 Z= 0.511 Chirality : 0.053 0.186 672 Planarity : 0.008 0.052 777 Dihedral : 14.772 89.587 1545 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.29), residues: 548 helix: -2.86 (0.25), residues: 219 sheet: 0.16 (0.44), residues: 118 loop : -2.90 (0.33), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 161 HIS 0.021 0.003 HIS A 98 PHE 0.025 0.002 PHE A 179 TYR 0.015 0.002 TYR C 143 ARG 0.030 0.002 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.17976 ( 226) hydrogen bonds : angle 6.50202 ( 636) covalent geometry : bond 0.00772 ( 4337) covalent geometry : angle 0.92351 ( 5888) Misc. bond : bond 0.11476 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.8732 (p) cc_final: 0.8463 (p) REVERT: A 194 ASP cc_start: 0.7743 (p0) cc_final: 0.7362 (p0) REVERT: B 78 GLU cc_start: 0.6959 (tp30) cc_final: 0.6723 (tp30) REVERT: B 151 ILE cc_start: 0.8523 (tt) cc_final: 0.8185 (tt) REVERT: C 94 GLN cc_start: 0.7756 (tt0) cc_final: 0.7469 (tt0) REVERT: C 122 ARG cc_start: 0.8390 (mmt90) cc_final: 0.8107 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2229 time to fit residues: 51.2446 Evaluate side-chains 151 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 124 HIS B 113 ASN B 124 HIS B 153 HIS B 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113214 restraints weight = 9093.996| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.30 r_work: 0.3269 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4339 Z= 0.126 Angle : 0.604 7.203 5888 Z= 0.322 Chirality : 0.042 0.155 672 Planarity : 0.005 0.041 777 Dihedral : 5.438 50.231 590 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.97 % Allowed : 13.50 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.75 (0.32), residues: 548 helix: -1.21 (0.30), residues: 235 sheet: 0.72 (0.44), residues: 117 loop : -2.17 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 161 HIS 0.004 0.001 HIS A 157 PHE 0.017 0.001 PHE C 100 TYR 0.010 0.001 TYR C 182 ARG 0.005 0.001 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 226) hydrogen bonds : angle 5.01611 ( 636) covalent geometry : bond 0.00283 ( 4337) covalent geometry : angle 0.60400 ( 5888) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9508 (t) cc_final: 0.9252 (p) REVERT: A 209 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 212 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8793 (ttp80) REVERT: B 67 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (p0) REVERT: B 68 GLU cc_start: 0.8391 (mp0) cc_final: 0.7943 (mp0) REVERT: B 118 TRP cc_start: 0.8357 (m-90) cc_final: 0.7638 (m-10) REVERT: B 151 ILE cc_start: 0.8529 (tt) cc_final: 0.7868 (tt) REVERT: C 96 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7700 (ttm170) REVERT: C 118 THR cc_start: 0.7921 (m) cc_final: 0.7310 (p) REVERT: C 216 ASP cc_start: 0.7577 (t0) cc_final: 0.7298 (p0) outliers start: 13 outliers final: 9 residues processed: 189 average time/residue: 0.2217 time to fit residues: 49.7989 Evaluate side-chains 167 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 188 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 9.9990 chunk 32 optimal weight: 0.0020 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 95 GLN A 120 GLN B 80 ASN B 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109788 restraints weight = 9161.724| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.32 r_work: 0.3223 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4339 Z= 0.169 Angle : 0.601 5.206 5888 Z= 0.326 Chirality : 0.043 0.213 672 Planarity : 0.005 0.038 777 Dihedral : 5.191 30.521 590 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.35 % Allowed : 18.31 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.02 (0.34), residues: 548 helix: -0.42 (0.32), residues: 235 sheet: 0.77 (0.45), residues: 117 loop : -1.81 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 118 HIS 0.010 0.001 HIS B 153 PHE 0.015 0.001 PHE C 165 TYR 0.013 0.002 TYR C 143 ARG 0.005 0.001 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 226) hydrogen bonds : angle 4.97779 ( 636) covalent geometry : bond 0.00391 ( 4337) covalent geometry : angle 0.60085 ( 5888) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (tpt) REVERT: A 170 VAL cc_start: 0.9542 (t) cc_final: 0.9303 (p) REVERT: A 194 ASP cc_start: 0.8627 (p0) cc_final: 0.8248 (p0) REVERT: A 209 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8215 (mm-30) REVERT: B 67 ASP cc_start: 0.8964 (p0) cc_final: 0.8744 (p0) REVERT: B 68 GLU cc_start: 0.8576 (mp0) cc_final: 0.8215 (mp0) REVERT: B 91 HIS cc_start: 0.8202 (m90) cc_final: 0.7898 (m-70) REVERT: B 113 ASN cc_start: 0.9179 (p0) cc_final: 0.8878 (p0) REVERT: B 118 TRP cc_start: 0.8313 (m-90) cc_final: 0.7715 (m-10) REVERT: B 149 ASP cc_start: 0.7779 (t0) cc_final: 0.7328 (t0) REVERT: B 151 ILE cc_start: 0.8251 (tt) cc_final: 0.7933 (tt) REVERT: B 209 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7974 (pt0) REVERT: C 88 MET cc_start: 0.8366 (mmm) cc_final: 0.8062 (mmm) REVERT: C 115 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 118 THR cc_start: 0.7840 (m) cc_final: 0.7255 (p) outliers start: 19 outliers final: 14 residues processed: 172 average time/residue: 0.1986 time to fit residues: 40.7783 Evaluate side-chains 171 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109840 restraints weight = 9395.511| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.33 r_work: 0.3221 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4339 Z= 0.171 Angle : 0.598 5.061 5888 Z= 0.324 Chirality : 0.043 0.220 672 Planarity : 0.005 0.037 777 Dihedral : 5.131 26.601 590 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.81 % Allowed : 23.34 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.35), residues: 548 helix: -0.10 (0.32), residues: 241 sheet: 0.77 (0.46), residues: 117 loop : -1.55 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 57 HIS 0.008 0.001 HIS B 153 PHE 0.016 0.001 PHE C 165 TYR 0.010 0.002 TYR C 143 ARG 0.005 0.001 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 226) hydrogen bonds : angle 4.95782 ( 636) covalent geometry : bond 0.00401 ( 4337) covalent geometry : angle 0.59842 ( 5888) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8424 (tpt) REVERT: A 170 VAL cc_start: 0.9551 (t) cc_final: 0.9317 (p) REVERT: A 194 ASP cc_start: 0.8546 (p0) cc_final: 0.8321 (p0) REVERT: A 209 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 212 ARG cc_start: 0.8963 (tmm-80) cc_final: 0.8402 (ttp80) REVERT: B 56 GLU cc_start: 0.8410 (tp30) cc_final: 0.8203 (tp30) REVERT: B 67 ASP cc_start: 0.8910 (p0) cc_final: 0.8677 (p0) REVERT: B 68 GLU cc_start: 0.8557 (mp0) cc_final: 0.8235 (mp0) REVERT: B 91 HIS cc_start: 0.8140 (m90) cc_final: 0.7793 (m-70) REVERT: B 118 TRP cc_start: 0.8284 (m-90) cc_final: 0.7871 (m-10) REVERT: B 149 ASP cc_start: 0.7782 (t0) cc_final: 0.7559 (t0) REVERT: B 151 ILE cc_start: 0.8290 (tt) cc_final: 0.8054 (tt) REVERT: B 195 ASN cc_start: 0.8117 (m-40) cc_final: 0.7218 (p0) REVERT: B 209 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8021 (pt0) REVERT: C 88 MET cc_start: 0.8304 (mmm) cc_final: 0.8042 (mmm) REVERT: C 115 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7215 (mt-10) REVERT: C 118 THR cc_start: 0.7942 (m) cc_final: 0.7384 (p) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 0.1973 time to fit residues: 39.2089 Evaluate side-chains 175 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113748 restraints weight = 9297.017| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.36 r_work: 0.3270 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4339 Z= 0.109 Angle : 0.550 6.116 5888 Z= 0.296 Chirality : 0.041 0.235 672 Planarity : 0.005 0.038 777 Dihedral : 4.797 36.971 590 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.12 % Allowed : 25.40 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.36), residues: 548 helix: 0.48 (0.34), residues: 230 sheet: 0.87 (0.47), residues: 117 loop : -1.27 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 161 HIS 0.007 0.001 HIS B 153 PHE 0.016 0.001 PHE C 165 TYR 0.007 0.001 TYR C 143 ARG 0.009 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 226) hydrogen bonds : angle 4.67778 ( 636) covalent geometry : bond 0.00243 ( 4337) covalent geometry : angle 0.54982 ( 5888) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9542 (t) cc_final: 0.9310 (p) REVERT: A 209 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 118 TRP cc_start: 0.8258 (m-90) cc_final: 0.7802 (m-10) REVERT: B 149 ASP cc_start: 0.7710 (t0) cc_final: 0.7436 (t0) REVERT: B 151 ILE cc_start: 0.8261 (tt) cc_final: 0.7914 (tt) REVERT: B 195 ASN cc_start: 0.7920 (m-40) cc_final: 0.7227 (p0) REVERT: B 209 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7898 (pt0) REVERT: C 88 MET cc_start: 0.8272 (mmm) cc_final: 0.8002 (mmm) REVERT: C 98 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8037 (mm) REVERT: C 115 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 118 THR cc_start: 0.7935 (m) cc_final: 0.7445 (p) outliers start: 18 outliers final: 12 residues processed: 167 average time/residue: 0.1858 time to fit residues: 37.6196 Evaluate side-chains 170 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113607 restraints weight = 9306.160| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.36 r_work: 0.3271 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4339 Z= 0.112 Angle : 0.568 8.776 5888 Z= 0.299 Chirality : 0.042 0.239 672 Planarity : 0.004 0.040 777 Dihedral : 4.815 36.547 590 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.58 % Allowed : 24.49 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.23 (0.36), residues: 548 helix: 0.74 (0.34), residues: 230 sheet: 1.09 (0.47), residues: 115 loop : -1.03 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.004 0.001 HIS B 157 PHE 0.015 0.001 PHE C 165 TYR 0.009 0.001 TYR C 200 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 226) hydrogen bonds : angle 4.61034 ( 636) covalent geometry : bond 0.00253 ( 4337) covalent geometry : angle 0.56752 ( 5888) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9550 (t) cc_final: 0.9344 (p) REVERT: A 174 TYR cc_start: 0.8810 (m-80) cc_final: 0.8538 (t80) REVERT: B 68 GLU cc_start: 0.8485 (mp0) cc_final: 0.8092 (mp0) REVERT: B 118 TRP cc_start: 0.8268 (m-90) cc_final: 0.7881 (m-10) REVERT: B 123 LEU cc_start: 0.9101 (tp) cc_final: 0.8899 (tp) REVERT: B 149 ASP cc_start: 0.7633 (t0) cc_final: 0.7400 (t0) REVERT: B 191 LEU cc_start: 0.9175 (mt) cc_final: 0.8895 (mp) REVERT: B 195 ASN cc_start: 0.7989 (m-40) cc_final: 0.7198 (p0) REVERT: B 209 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7934 (pt0) REVERT: C 88 MET cc_start: 0.8218 (mmm) cc_final: 0.7993 (mmm) REVERT: C 115 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 118 THR cc_start: 0.7923 (m) cc_final: 0.7467 (p) outliers start: 20 outliers final: 16 residues processed: 168 average time/residue: 0.1917 time to fit residues: 38.6361 Evaluate side-chains 165 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112757 restraints weight = 9370.631| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.36 r_work: 0.3259 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4339 Z= 0.133 Angle : 0.595 9.185 5888 Z= 0.312 Chirality : 0.042 0.252 672 Planarity : 0.004 0.038 777 Dihedral : 4.788 35.180 590 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.35 % Allowed : 25.17 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.31 (0.36), residues: 548 helix: 0.88 (0.35), residues: 228 sheet: 1.05 (0.46), residues: 115 loop : -1.02 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.004 0.001 HIS B 153 PHE 0.015 0.001 PHE C 165 TYR 0.007 0.001 TYR C 151 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 226) hydrogen bonds : angle 4.67874 ( 636) covalent geometry : bond 0.00311 ( 4337) covalent geometry : angle 0.59461 ( 5888) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9551 (t) cc_final: 0.9321 (p) REVERT: A 174 TYR cc_start: 0.8799 (m-80) cc_final: 0.8483 (t80) REVERT: B 91 HIS cc_start: 0.7986 (m90) cc_final: 0.7716 (m-70) REVERT: B 113 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8899 (p0) REVERT: B 118 TRP cc_start: 0.8279 (m-90) cc_final: 0.7893 (m-10) REVERT: B 149 ASP cc_start: 0.7778 (t0) cc_final: 0.7546 (t0) REVERT: B 191 LEU cc_start: 0.9181 (mt) cc_final: 0.8930 (mp) REVERT: B 195 ASN cc_start: 0.7925 (m-40) cc_final: 0.7245 (p0) REVERT: C 88 MET cc_start: 0.8230 (mmm) cc_final: 0.8024 (mmm) REVERT: C 115 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7261 (mt-10) REVERT: C 118 THR cc_start: 0.7926 (m) cc_final: 0.7440 (p) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.2038 time to fit residues: 38.5950 Evaluate side-chains 161 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.0010 chunk 48 optimal weight: 0.0020 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115363 restraints weight = 9223.473| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.33 r_work: 0.3294 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4339 Z= 0.113 Angle : 0.579 7.805 5888 Z= 0.304 Chirality : 0.042 0.230 672 Planarity : 0.004 0.041 777 Dihedral : 4.708 38.030 590 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.89 % Allowed : 26.54 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.38 (0.36), residues: 548 helix: 0.91 (0.35), residues: 228 sheet: 1.13 (0.46), residues: 115 loop : -0.97 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 161 HIS 0.003 0.001 HIS B 157 PHE 0.017 0.001 PHE C 165 TYR 0.009 0.001 TYR C 200 ARG 0.007 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 226) hydrogen bonds : angle 4.57044 ( 636) covalent geometry : bond 0.00258 ( 4337) covalent geometry : angle 0.57875 ( 5888) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TYR cc_start: 0.8834 (m-80) cc_final: 0.8548 (t80) REVERT: B 118 TRP cc_start: 0.8262 (m-90) cc_final: 0.7821 (m-10) REVERT: B 149 ASP cc_start: 0.7632 (t0) cc_final: 0.7393 (t0) REVERT: B 191 LEU cc_start: 0.9165 (mt) cc_final: 0.8927 (mp) REVERT: B 195 ASN cc_start: 0.7963 (m-40) cc_final: 0.7230 (p0) REVERT: C 88 MET cc_start: 0.8218 (mmm) cc_final: 0.8015 (mmm) REVERT: C 115 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 118 THR cc_start: 0.7968 (m) cc_final: 0.7506 (p) REVERT: C 145 PHE cc_start: 0.8760 (t80) cc_final: 0.8526 (t80) outliers start: 17 outliers final: 16 residues processed: 159 average time/residue: 0.2027 time to fit residues: 39.0890 Evaluate side-chains 157 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111895 restraints weight = 9509.893| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.33 r_work: 0.3256 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4339 Z= 0.138 Angle : 0.623 9.912 5888 Z= 0.321 Chirality : 0.043 0.229 672 Planarity : 0.004 0.039 777 Dihedral : 4.777 34.577 590 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.12 % Allowed : 26.77 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.50 (0.36), residues: 548 helix: 1.03 (0.35), residues: 226 sheet: 1.08 (0.46), residues: 115 loop : -0.84 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 118 HIS 0.004 0.001 HIS A 131 PHE 0.015 0.001 PHE C 165 TYR 0.007 0.001 TYR C 151 ARG 0.005 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 226) hydrogen bonds : angle 4.69572 ( 636) covalent geometry : bond 0.00329 ( 4337) covalent geometry : angle 0.62288 ( 5888) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 91 HIS cc_start: 0.7993 (m90) cc_final: 0.7721 (m-70) REVERT: B 113 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8884 (p0) REVERT: B 118 TRP cc_start: 0.8204 (m-90) cc_final: 0.7907 (m100) REVERT: B 149 ASP cc_start: 0.7787 (t0) cc_final: 0.7545 (t0) REVERT: B 191 LEU cc_start: 0.9188 (mt) cc_final: 0.8964 (mp) REVERT: B 195 ASN cc_start: 0.8041 (m-40) cc_final: 0.7203 (p0) REVERT: B 209 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: C 88 MET cc_start: 0.8272 (mmm) cc_final: 0.8059 (mmm) REVERT: C 115 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 118 THR cc_start: 0.7882 (m) cc_final: 0.7384 (p) REVERT: C 215 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8294 (mtm110) outliers start: 18 outliers final: 14 residues processed: 148 average time/residue: 0.1999 time to fit residues: 35.5515 Evaluate side-chains 159 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112211 restraints weight = 9308.013| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.32 r_work: 0.3259 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 4339 Z= 0.203 Angle : 1.165 59.198 5888 Z= 0.679 Chirality : 0.044 0.256 672 Planarity : 0.005 0.073 777 Dihedral : 4.920 34.481 590 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.89 % Allowed : 27.00 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.53 (0.36), residues: 548 helix: 1.05 (0.35), residues: 226 sheet: 1.08 (0.46), residues: 115 loop : -0.83 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.005 0.001 HIS A 131 PHE 0.017 0.001 PHE C 165 TYR 0.007 0.001 TYR C 151 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 226) hydrogen bonds : angle 4.69890 ( 636) covalent geometry : bond 0.00482 ( 4337) covalent geometry : angle 1.16455 ( 5888) Misc. bond : bond 0.00031 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 91 HIS cc_start: 0.7989 (m90) cc_final: 0.7711 (m-70) REVERT: B 118 TRP cc_start: 0.8206 (m-90) cc_final: 0.7908 (m100) REVERT: B 149 ASP cc_start: 0.7761 (t0) cc_final: 0.7519 (t0) REVERT: B 191 LEU cc_start: 0.9181 (mt) cc_final: 0.8963 (mp) REVERT: B 195 ASN cc_start: 0.8068 (m-40) cc_final: 0.7235 (p0) REVERT: B 209 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: C 88 MET cc_start: 0.8286 (mmm) cc_final: 0.8074 (mmm) REVERT: C 115 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 118 THR cc_start: 0.7878 (m) cc_final: 0.7383 (p) REVERT: C 145 PHE cc_start: 0.8819 (t80) cc_final: 0.8526 (t80) REVERT: C 215 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8287 (mtm110) outliers start: 17 outliers final: 15 residues processed: 150 average time/residue: 0.2029 time to fit residues: 36.6329 Evaluate side-chains 155 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 20 optimal weight: 0.0070 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.128652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112376 restraints weight = 9331.377| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.31 r_work: 0.3260 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 4339 Z= 0.203 Angle : 1.165 59.198 5888 Z= 0.679 Chirality : 0.044 0.256 672 Planarity : 0.005 0.073 777 Dihedral : 4.920 34.481 590 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.66 % Allowed : 27.23 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.53 (0.36), residues: 548 helix: 1.05 (0.35), residues: 226 sheet: 1.08 (0.46), residues: 115 loop : -0.83 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.005 0.001 HIS A 131 PHE 0.017 0.001 PHE C 165 TYR 0.007 0.001 TYR C 151 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 226) hydrogen bonds : angle 4.69890 ( 636) covalent geometry : bond 0.00482 ( 4337) covalent geometry : angle 1.16455 ( 5888) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.43 seconds wall clock time: 43 minutes 48.00 seconds (2628.00 seconds total)