Starting phenix.real_space_refine on Wed Sep 17 04:35:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irv_60822/09_2025/9irv_60822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irv_60822/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9irv_60822/09_2025/9irv_60822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irv_60822/09_2025/9irv_60822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9irv_60822/09_2025/9irv_60822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irv_60822/09_2025/9irv_60822.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.27, per 1000 atoms: 0.30 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: 0.40 Conformation dependent library (CDL) restraints added in 187.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.59 Time building geometry restraints manager: 0.51 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: 2.330 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.030 0.002 ARG B 62 TYR 0.015 0.002 TYR C 143 PHE 0.025 0.002 PHE A 179 TRP 0.017 0.003 TRP B 161 HIS 0.021 0.003 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 4337) covalent geometry : angle 0.92351 ( 5888) hydrogen bonds : bond 0.17976 ( 226) hydrogen bonds : angle 6.50202 ( 636) 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 : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.8732 (p) cc_final: 0.8464 (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: 0.1066 time to fit residues: 24.4096 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 91 HIS B 113 ASN B 124 HIS B 153 HIS B 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112675 restraints weight = 9157.640| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.29 r_work: 0.3254 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4339 Z= 0.136 Angle : 0.614 7.158 5888 Z= 0.328 Chirality : 0.042 0.156 672 Planarity : 0.005 0.041 777 Dihedral : 5.465 48.017 590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.97 % Allowed : 13.73 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.32), residues: 548 helix: -1.19 (0.30), residues: 233 sheet: 0.70 (0.44), residues: 117 loop : -2.07 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.010 0.001 TYR C 182 PHE 0.013 0.001 PHE C 100 TRP 0.009 0.001 TRP B 161 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4337) covalent geometry : angle 0.61385 ( 5888) hydrogen bonds : bond 0.04093 ( 226) hydrogen bonds : angle 5.05894 ( 636) Misc. bond : bond 0.00067 ( 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 195 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9513 (t) cc_final: 0.9257 (p) REVERT: A 209 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 212 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8810 (ttp80) REVERT: B 67 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8670 (p0) REVERT: B 68 GLU cc_start: 0.8435 (mp0) cc_final: 0.7941 (mp0) REVERT: B 96 ARG cc_start: 0.8343 (mtt90) cc_final: 0.7832 (mmm-85) REVERT: B 118 TRP cc_start: 0.8354 (m-90) cc_final: 0.7682 (m-10) REVERT: B 151 ILE cc_start: 0.8536 (tt) cc_final: 0.7959 (tt) REVERT: B 209 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8088 (pt0) REVERT: C 115 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7005 (mt-10) REVERT: C 118 THR cc_start: 0.7922 (m) cc_final: 0.7291 (p) REVERT: C 216 ASP cc_start: 0.7573 (t0) cc_final: 0.7266 (p0) outliers start: 13 outliers final: 9 residues processed: 186 average time/residue: 0.0934 time to fit residues: 20.6790 Evaluate side-chains 170 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 23 optimal weight: 8.9990 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 0.0870 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 1.4160 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110380 restraints weight = 9251.174| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.33 r_work: 0.3229 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3069 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= 0.151 Angle : 0.597 5.210 5888 Z= 0.323 Chirality : 0.043 0.199 672 Planarity : 0.005 0.038 777 Dihedral : 5.126 28.156 590 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.35 % Allowed : 17.85 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.34), residues: 548 helix: -0.36 (0.32), residues: 235 sheet: 0.79 (0.45), residues: 117 loop : -1.78 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.010 0.001 TYR C 143 PHE 0.015 0.001 PHE C 165 TRP 0.006 0.001 TRP B 161 HIS 0.010 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4337) covalent geometry : angle 0.59703 ( 5888) hydrogen bonds : bond 0.03970 ( 226) hydrogen bonds : angle 4.94708 ( 636) Misc. bond : bond 0.00062 ( 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 192 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8383 (tpt) REVERT: A 170 VAL cc_start: 0.9536 (t) cc_final: 0.9296 (p) REVERT: A 194 ASP cc_start: 0.8588 (p0) cc_final: 0.8162 (p0) REVERT: A 209 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8234 (mm-30) REVERT: B 56 GLU cc_start: 0.8382 (tp30) cc_final: 0.7923 (tp30) REVERT: B 67 ASP cc_start: 0.8947 (p0) cc_final: 0.8605 (p0) REVERT: B 68 GLU cc_start: 0.8595 (mp0) cc_final: 0.8134 (mp0) REVERT: B 91 HIS cc_start: 0.8208 (m90) cc_final: 0.7910 (m90) REVERT: B 118 TRP cc_start: 0.8358 (m-90) cc_final: 0.7654 (m-10) REVERT: B 209 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8096 (pt0) REVERT: C 88 MET cc_start: 0.8342 (mmm) cc_final: 0.8038 (mmm) REVERT: C 100 PHE cc_start: 0.8505 (m-80) cc_final: 0.8258 (m-10) REVERT: C 115 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 118 THR cc_start: 0.7866 (m) cc_final: 0.7396 (p) outliers start: 19 outliers final: 14 residues processed: 179 average time/residue: 0.0888 time to fit residues: 19.0295 Evaluate side-chains 167 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 95 GLN B 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109140 restraints weight = 9316.997| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.35 r_work: 0.3212 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3381 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= 0.161 Angle : 0.586 5.066 5888 Z= 0.318 Chirality : 0.043 0.221 672 Planarity : 0.004 0.037 777 Dihedral : 5.086 31.825 590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.49 % Allowed : 21.28 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.35), residues: 548 helix: 0.07 (0.33), residues: 235 sheet: 0.79 (0.46), residues: 117 loop : -1.52 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 215 TYR 0.009 0.001 TYR C 143 PHE 0.015 0.001 PHE C 165 TRP 0.008 0.001 TRP B 161 HIS 0.003 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4337) covalent geometry : angle 0.58560 ( 5888) hydrogen bonds : bond 0.03866 ( 226) hydrogen bonds : angle 4.88586 ( 636) Misc. bond : bond 0.00079 ( 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 178 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8318 (tpt) REVERT: A 170 VAL cc_start: 0.9541 (t) cc_final: 0.9313 (p) REVERT: A 194 ASP cc_start: 0.8565 (p0) cc_final: 0.8272 (p0) REVERT: A 209 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 212 ARG cc_start: 0.9025 (tmm-80) cc_final: 0.8523 (ttp80) REVERT: B 67 ASP cc_start: 0.8892 (p0) cc_final: 0.8535 (p0) REVERT: B 68 GLU cc_start: 0.8540 (mp0) cc_final: 0.8111 (mp0) REVERT: B 91 HIS cc_start: 0.8201 (m90) cc_final: 0.7864 (m-70) REVERT: B 118 TRP cc_start: 0.8341 (m-90) cc_final: 0.7826 (m-10) REVERT: B 149 ASP cc_start: 0.8009 (t0) cc_final: 0.7741 (t0) REVERT: B 209 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8121 (pt0) REVERT: C 88 MET cc_start: 0.8319 (mmm) cc_final: 0.8046 (mmm) REVERT: C 115 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 118 THR cc_start: 0.7895 (m) cc_final: 0.7323 (p) outliers start: 24 outliers final: 17 residues processed: 162 average time/residue: 0.0920 time to fit residues: 17.9645 Evaluate side-chains 164 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 210 CYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 18 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN B 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111233 restraints weight = 9269.828| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.37 r_work: 0.3245 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3628 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= 0.119 Angle : 0.558 5.767 5888 Z= 0.301 Chirality : 0.042 0.242 672 Planarity : 0.004 0.038 777 Dihedral : 4.916 42.077 590 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.36), residues: 548 helix: 0.39 (0.34), residues: 236 sheet: 0.91 (0.47), residues: 117 loop : -1.23 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.006 0.001 TYR C 182 PHE 0.017 0.001 PHE C 100 TRP 0.007 0.001 TRP B 161 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4337) covalent geometry : angle 0.55783 ( 5888) hydrogen bonds : bond 0.03373 ( 226) hydrogen bonds : angle 4.68553 ( 636) Misc. bond : bond 0.00043 ( 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 183 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (tpt) REVERT: A 170 VAL cc_start: 0.9540 (t) cc_final: 0.9316 (p) REVERT: A 194 ASP cc_start: 0.8424 (p0) cc_final: 0.8130 (p0) REVERT: A 209 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 91 HIS cc_start: 0.8062 (m90) cc_final: 0.7794 (m-70) REVERT: B 118 TRP cc_start: 0.8295 (m-90) cc_final: 0.7725 (m-10) REVERT: B 195 ASN cc_start: 0.7793 (m110) cc_final: 0.7055 (p0) REVERT: B 209 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8166 (pt0) REVERT: C 88 MET cc_start: 0.8312 (mmm) cc_final: 0.8056 (mmm) REVERT: C 115 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 118 THR cc_start: 0.7841 (m) cc_final: 0.7323 (p) outliers start: 20 outliers final: 12 residues processed: 167 average time/residue: 0.0882 time to fit residues: 17.6887 Evaluate side-chains 171 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 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 208 LEU Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.128174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111484 restraints weight = 9436.265| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.37 r_work: 0.3242 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4339 Z= 0.128 Angle : 0.568 5.887 5888 Z= 0.304 Chirality : 0.043 0.249 672 Planarity : 0.004 0.038 777 Dihedral : 4.963 39.449 590 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.81 % Allowed : 24.49 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.36), residues: 548 helix: 0.74 (0.35), residues: 230 sheet: 1.09 (0.47), residues: 115 loop : -1.08 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.009 0.001 TYR C 200 PHE 0.017 0.001 PHE C 165 TRP 0.005 0.001 TRP A 161 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4337) covalent geometry : angle 0.56815 ( 5888) hydrogen bonds : bond 0.03423 ( 226) hydrogen bonds : angle 4.78515 ( 636) Misc. bond : bond 0.00054 ( 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 181 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9547 (t) cc_final: 0.9326 (p) REVERT: A 209 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 68 GLU cc_start: 0.8477 (mp0) cc_final: 0.8085 (mp0) REVERT: B 118 TRP cc_start: 0.8341 (m-90) cc_final: 0.7795 (m100) REVERT: B 195 ASN cc_start: 0.7717 (m110) cc_final: 0.7139 (p0) REVERT: B 199 ASP cc_start: 0.8154 (p0) cc_final: 0.7902 (p0) REVERT: B 209 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8195 (pt0) REVERT: C 88 MET cc_start: 0.8293 (mmm) cc_final: 0.8034 (mmm) REVERT: C 115 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7224 (mt-10) REVERT: C 118 THR cc_start: 0.7880 (m) cc_final: 0.7327 (p) outliers start: 21 outliers final: 14 residues processed: 168 average time/residue: 0.0880 time to fit residues: 17.7742 Evaluate side-chains 167 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP 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 208 LEU Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110602 restraints weight = 9434.016| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.37 r_work: 0.3230 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4339 Z= 0.146 Angle : 0.598 8.907 5888 Z= 0.315 Chirality : 0.043 0.246 672 Planarity : 0.004 0.040 777 Dihedral : 4.977 36.360 590 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.03 % Allowed : 24.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.36), residues: 548 helix: 0.88 (0.35), residues: 230 sheet: 1.13 (0.47), residues: 115 loop : -1.04 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.007 0.001 TYR C 151 PHE 0.016 0.001 PHE C 165 TRP 0.007 0.001 TRP B 161 HIS 0.015 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4337) covalent geometry : angle 0.59824 ( 5888) hydrogen bonds : bond 0.03607 ( 226) hydrogen bonds : angle 4.80209 ( 636) Misc. bond : bond 0.00063 ( 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 176 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9547 (t) cc_final: 0.9324 (p) REVERT: B 118 TRP cc_start: 0.8335 (m-90) cc_final: 0.7897 (m100) REVERT: B 195 ASN cc_start: 0.7880 (m-40) cc_final: 0.7106 (p0) REVERT: B 209 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8062 (pt0) REVERT: C 88 MET cc_start: 0.8270 (mmm) cc_final: 0.8063 (mmm) REVERT: C 115 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 118 THR cc_start: 0.7828 (m) cc_final: 0.7302 (p) outliers start: 22 outliers final: 15 residues processed: 161 average time/residue: 0.0872 time to fit residues: 16.7650 Evaluate side-chains 163 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111356 restraints weight = 9442.546| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.37 r_work: 0.3227 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4339 Z= 0.152 Angle : 0.610 7.086 5888 Z= 0.323 Chirality : 0.045 0.252 672 Planarity : 0.004 0.041 777 Dihedral : 5.027 36.241 590 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.36), residues: 548 helix: 0.91 (0.35), residues: 230 sheet: 1.08 (0.47), residues: 115 loop : -0.99 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.009 0.001 TYR C 200 PHE 0.023 0.002 PHE C 165 TRP 0.009 0.001 TRP B 161 HIS 0.012 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4337) covalent geometry : angle 0.61033 ( 5888) hydrogen bonds : bond 0.03684 ( 226) hydrogen bonds : angle 4.84124 ( 636) Misc. bond : bond 0.00066 ( 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 168 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9556 (t) cc_final: 0.9334 (p) REVERT: A 209 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 212 ARG cc_start: 0.8921 (tmm-80) cc_final: 0.8502 (ttp80) REVERT: B 183 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7966 (mtpt) REVERT: B 195 ASN cc_start: 0.7956 (m-40) cc_final: 0.7234 (p0) REVERT: B 209 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8271 (tm-30) REVERT: C 115 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7222 (mt-10) REVERT: C 118 THR cc_start: 0.7912 (m) cc_final: 0.7463 (p) REVERT: C 215 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8236 (mtm110) outliers start: 17 outliers final: 15 residues processed: 156 average time/residue: 0.0916 time to fit residues: 17.1038 Evaluate side-chains 158 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.129742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113296 restraints weight = 9526.053| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.40 r_work: 0.3266 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4339 Z= 0.126 Angle : 0.648 8.401 5888 Z= 0.337 Chirality : 0.044 0.264 672 Planarity : 0.005 0.041 777 Dihedral : 4.970 45.871 590 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 29.29 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.36), residues: 548 helix: 0.86 (0.35), residues: 230 sheet: 1.15 (0.47), residues: 115 loop : -0.89 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.008 0.001 TYR C 200 PHE 0.017 0.001 PHE C 100 TRP 0.005 0.001 TRP B 161 HIS 0.012 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4337) covalent geometry : angle 0.64802 ( 5888) hydrogen bonds : bond 0.03316 ( 226) hydrogen bonds : angle 4.80083 ( 636) Misc. bond : bond 0.00042 ( 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 168 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 170 VAL cc_start: 0.9552 (t) cc_final: 0.9343 (p) REVERT: B 118 TRP cc_start: 0.8369 (m-90) cc_final: 0.7870 (m100) REVERT: B 183 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7972 (mtpt) REVERT: B 195 ASN cc_start: 0.7970 (m-40) cc_final: 0.7177 (p0) REVERT: B 209 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8136 (pt0) REVERT: C 115 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 118 THR cc_start: 0.7818 (m) cc_final: 0.7344 (p) outliers start: 12 outliers final: 11 residues processed: 161 average time/residue: 0.0851 time to fit residues: 16.5343 Evaluate side-chains 157 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113839 restraints weight = 9399.918| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.34 r_work: 0.3281 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4339 Z= 0.135 Angle : 0.668 9.217 5888 Z= 0.348 Chirality : 0.045 0.277 672 Planarity : 0.005 0.041 777 Dihedral : 5.030 45.358 590 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.97 % Allowed : 30.43 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.36), residues: 548 helix: 0.84 (0.35), residues: 230 sheet: 1.08 (0.46), residues: 115 loop : -0.82 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 212 TYR 0.008 0.001 TYR C 200 PHE 0.029 0.001 PHE C 165 TRP 0.005 0.001 TRP B 161 HIS 0.012 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4337) covalent geometry : angle 0.66779 ( 5888) hydrogen bonds : bond 0.03395 ( 226) hydrogen bonds : angle 4.86683 ( 636) Misc. bond : bond 0.00045 ( 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 161 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8335 (tt) cc_final: 0.7855 (tt) REVERT: A 170 VAL cc_start: 0.9560 (t) cc_final: 0.9347 (p) REVERT: A 194 ASP cc_start: 0.8663 (p0) cc_final: 0.8212 (p0) REVERT: B 150 ASN cc_start: 0.8546 (m110) cc_final: 0.8119 (p0) REVERT: B 183 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7950 (mtpt) REVERT: B 195 ASN cc_start: 0.7960 (m-40) cc_final: 0.7154 (p0) REVERT: B 209 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8182 (pt0) REVERT: C 96 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7464 (ttm170) REVERT: C 115 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 118 THR cc_start: 0.7907 (m) cc_final: 0.7468 (p) outliers start: 13 outliers final: 12 residues processed: 153 average time/residue: 0.0880 time to fit residues: 16.1841 Evaluate side-chains 156 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 199 ASP Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 5 GLU 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 Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.0020 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 0.3644 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116456 restraints weight = 9285.824| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.37 r_work: 0.3314 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4339 Z= 0.119 Angle : 0.650 9.534 5888 Z= 0.336 Chirality : 0.043 0.284 672 Planarity : 0.005 0.044 777 Dihedral : 4.909 52.317 590 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.75 % Allowed : 30.43 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.37), residues: 548 helix: 0.84 (0.35), residues: 234 sheet: 1.14 (0.46), residues: 115 loop : -0.65 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.005 0.001 TYR B 174 PHE 0.024 0.001 PHE C 165 TRP 0.005 0.000 TRP A 161 HIS 0.011 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4337) covalent geometry : angle 0.64966 ( 5888) hydrogen bonds : bond 0.02979 ( 226) hydrogen bonds : angle 4.73619 ( 636) Misc. bond : bond 0.00025 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.89 seconds wall clock time: 22 minutes 16.30 seconds (1336.30 seconds total)