Starting phenix.real_space_refine on Tue Aug 4 16:01:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939.map" model { file = "/net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zy0_74939/08_2026/9zy0_74939_neut.cif" } resolution = 3.2 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 16 5.49 5 S 28 5.16 5 C 2842 2.51 5 N 807 2.21 5 O 862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4557 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1443 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1249 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1526 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 172} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna3p_pyr': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 986 SG CYS A 116 22.081 24.181 69.939 1.00101.94 S ATOM 1131 SG CYS A 135 24.434 22.955 67.238 1.00 93.61 S Time building chain proxies: 1.25, per 1000 atoms: 0.27 Number of scatterers: 4557 At special positions: 0 Unit cell: (78.6144, 78.6144, 94.1735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 16 15.00 O 862 8.00 N 807 7.00 C 2842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 159.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 116 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 135 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 110 " 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 42.2% alpha, 25.0% beta 7 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.027A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 15 through 23 removed outlier: 4.067A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 54 through 67 removed outlier: 3.971A pdb=" N GLY C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 158 through 183 removed outlier: 3.854A pdb=" N MET C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE A 89 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 13.653A pdb=" N TRP A 91 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 16.277A pdb=" N VAL A 9 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU B 64 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 120 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.660A pdb=" N SER A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N TRP A 97 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 102 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 47 removed outlier: 6.861A pdb=" N TRP C 82 " --> pdb=" O SER C 109 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1402 1.34 - 1.45: 872 1.45 - 1.57: 2367 1.57 - 1.69: 30 1.69 - 1.81: 36 Bond restraints: 4707 Sorted by residual: bond pdb=" N VAL C 76 " pdb=" CA VAL C 76 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" N TYR C 74 " pdb=" CA TYR C 74 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.10e+00 bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.23e-02 6.61e+03 6.05e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N VAL B 5 " pdb=" CA VAL B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 4702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 6112 1.23 - 2.45: 263 2.45 - 3.68: 45 3.68 - 4.90: 10 4.90 - 6.13: 3 Bond angle restraints: 6433 Sorted by residual: angle pdb=" CB GLU B 129 " pdb=" CG GLU B 129 " pdb=" CD GLU B 129 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.70e+00 3.46e-01 1.22e+01 angle pdb=" O5' U D 5 " pdb=" C5' U D 5 " pdb=" C4' U D 5 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" CA VAL C 76 " pdb=" C VAL C 76 " pdb=" O VAL C 76 " ideal model delta sigma weight residual 120.53 117.05 3.48 1.07e+00 8.73e-01 1.06e+01 angle pdb=" O5' U D 6 " pdb=" C5' U D 6 " pdb=" C4' U D 6 " ideal model delta sigma weight residual 109.40 111.95 -2.55 8.00e-01 1.56e+00 1.01e+01 angle pdb=" O5' U D 8 " pdb=" C5' U D 8 " pdb=" C4' U D 8 " ideal model delta sigma weight residual 109.40 111.94 -2.54 8.00e-01 1.56e+00 1.01e+01 ... (remaining 6428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 2499 16.16 - 32.32: 213 32.32 - 48.48: 68 48.48 - 64.64: 20 64.64 - 80.80: 3 Dihedral angle restraints: 2803 sinusoidal: 1312 harmonic: 1491 Sorted by residual: dihedral pdb=" CA ASN C 103 " pdb=" C ASN C 103 " pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta harmonic sigma weight residual 180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PHE B 69 " pdb=" C PHE B 69 " pdb=" N PRO B 70 " pdb=" CA PRO B 70 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 99 " pdb=" CB ASP A 99 " pdb=" CG ASP A 99 " pdb=" OD1 ASP A 99 " ideal model delta sinusoidal sigma weight residual -30.00 -86.13 56.13 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 2800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 408 0.029 - 0.059: 174 0.059 - 0.088: 42 0.088 - 0.118: 40 0.118 - 0.147: 15 Chirality restraints: 679 Sorted by residual: chirality pdb=" CA ILE A 8 " pdb=" N ILE A 8 " pdb=" C ILE A 8 " pdb=" CB ILE A 8 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 676 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 59 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 60 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 73 " -0.015 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP A 73 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 73 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 73 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 73 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 73 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 73 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 73 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 212 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" CD GLU A 212 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 212 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 212 " -0.010 2.00e-02 2.50e+03 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1310 2.82 - 3.34: 4288 3.34 - 3.86: 7614 3.86 - 4.38: 8986 4.38 - 4.90: 14896 Nonbonded interactions: 37094 Sorted by model distance: nonbonded pdb=" O GLU A 212 " pdb=" OE1 GLU A 212 " model vdw 2.302 3.040 nonbonded pdb=" O ASN A 74 " pdb=" OD1 ASN A 74 " model vdw 2.381 3.040 nonbonded pdb=" O LEU C 166 " pdb=" OD1 ASN C 169 " model vdw 2.400 3.040 nonbonded pdb=" OD1 ASP A 106 " pdb=" OH TYR A 137 " model vdw 2.406 3.040 nonbonded pdb=" N GLN C 119 " pdb=" OE1 GLN C 119 " model vdw 2.495 3.120 ... (remaining 37089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.040 Find NCS groups from input model: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.004 0.034 4710 Z= 0.183 Angle : 0.598 6.128 6433 Z= 0.358 Chirality : 0.043 0.147 679 Planarity : 0.006 0.060 771 Dihedral : 13.926 80.803 1837 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.38), residues: 501 helix: 1.19 (0.40), residues: 187 sheet: -0.86 (0.46), residues: 114 loop : -0.37 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 105 TYR 0.019 0.001 TYR A 72 PHE 0.014 0.002 PHE B 68 TRP 0.029 0.002 TRP A 73 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 ( 4707) covalent geometry : angle 0.59788 / 0.36 ( 6433) hydrogen bonds : bond 0.12951 / 8.72 ( 226) hydrogen bonds : angle 7.15724 / 4.95 ( 676) metal coordination : bond 0.01056 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.161 Fit side-chains REVERT: A 64 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7667 (ppt170) REVERT: B 85 TYR cc_start: 0.8603 (m-10) cc_final: 0.8276 (m-10) REVERT: B 118 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8277 (mtp-110) REVERT: C 18 ARG cc_start: 0.7108 (mmm160) cc_final: 0.6844 (mmp80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0983 time to fit residues: 10.6131 Evaluate side-chains 75 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.158147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133575 restraints weight = 6864.772| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.88 r_work: 0.3823 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4710 Z= 0.152 Angle : 0.575 6.243 6433 Z= 0.303 Chirality : 0.041 0.139 679 Planarity : 0.005 0.050 771 Dihedral : 9.115 58.445 786 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.55 % Allowed : 8.43 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.39), residues: 501 helix: 1.37 (0.39), residues: 198 sheet: -0.63 (0.47), residues: 112 loop : -0.08 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.016 0.002 TYR A 72 PHE 0.019 0.002 PHE C 9 TRP 0.012 0.001 TRP A 73 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4707) covalent geometry : angle 0.57456 / 0.30 ( 6433) hydrogen bonds : bond 0.04214 / 2.93 ( 226) hydrogen bonds : angle 5.58236 / 3.90 ( 676) metal coordination : bond 0.00294 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.278 Fit side-chains REVERT: A 64 ARG cc_start: 0.8202 (ptp-110) cc_final: 0.7335 (ptm-80) REVERT: A 212 GLU cc_start: 0.8484 (pp20) cc_final: 0.8233 (pp20) REVERT: B 118 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8256 (mtp-110) REVERT: B 129 GLU cc_start: 0.7807 (pm20) cc_final: 0.7521 (pm20) REVERT: C 66 MET cc_start: 0.5923 (mtp) cc_final: 0.5452 (mtt) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.1022 time to fit residues: 10.1010 Evaluate side-chains 76 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain C residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.155002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130742 restraints weight = 6921.649| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.83 r_work: 0.3790 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4710 Z= 0.193 Angle : 0.579 6.793 6433 Z= 0.309 Chirality : 0.041 0.152 679 Planarity : 0.005 0.050 771 Dihedral : 9.116 58.457 786 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.33 % Allowed : 11.75 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.38), residues: 501 helix: 1.29 (0.39), residues: 197 sheet: -0.80 (0.47), residues: 114 loop : -0.18 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.010 0.002 TYR B 85 PHE 0.018 0.002 PHE C 9 TRP 0.015 0.002 TRP A 73 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 4707) covalent geometry : angle 0.57910 / 0.31 ( 6433) hydrogen bonds : bond 0.04086 / 2.83 ( 226) hydrogen bonds : angle 5.38155 / 3.78 ( 676) metal coordination : bond 0.00264 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.167 Fit side-chains REVERT: A 64 ARG cc_start: 0.8310 (ptp-110) cc_final: 0.7667 (ppt170) REVERT: A 81 TRP cc_start: 0.7401 (t-100) cc_final: 0.6844 (t-100) REVERT: A 212 GLU cc_start: 0.8516 (pp20) cc_final: 0.8231 (pp20) REVERT: B 110 TRP cc_start: 0.7947 (t60) cc_final: 0.7671 (t60) REVERT: B 118 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8222 (mtp-110) REVERT: B 129 GLU cc_start: 0.7831 (pm20) cc_final: 0.7543 (pm20) REVERT: C 66 MET cc_start: 0.5906 (mtp) cc_final: 0.5478 (mtt) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.1011 time to fit residues: 9.4379 Evaluate side-chains 74 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.131422 restraints weight = 6963.447| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.87 r_work: 0.3796 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4710 Z= 0.150 Angle : 0.550 6.352 6433 Z= 0.289 Chirality : 0.040 0.148 679 Planarity : 0.005 0.051 771 Dihedral : 9.069 58.519 786 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.33 % Allowed : 13.75 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.38), residues: 501 helix: 1.44 (0.38), residues: 191 sheet: -0.71 (0.47), residues: 114 loop : -0.02 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.011 0.001 TYR B 85 PHE 0.018 0.002 PHE C 59 TRP 0.013 0.001 TRP A 73 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4707) covalent geometry : angle 0.55029 / 0.29 ( 6433) hydrogen bonds : bond 0.03749 / 2.61 ( 226) hydrogen bonds : angle 5.20998 / 3.64 ( 676) metal coordination : bond 0.00196 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: A 64 ARG cc_start: 0.8341 (ptp-110) cc_final: 0.7730 (ppt170) REVERT: A 81 TRP cc_start: 0.7396 (t-100) cc_final: 0.6903 (t-100) REVERT: A 212 GLU cc_start: 0.8490 (pp20) cc_final: 0.8131 (pp20) REVERT: B 110 TRP cc_start: 0.7955 (t60) cc_final: 0.7626 (t60) REVERT: B 118 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8176 (mtp-110) REVERT: B 129 GLU cc_start: 0.7812 (pm20) cc_final: 0.7515 (pm20) REVERT: C 66 MET cc_start: 0.5966 (mtp) cc_final: 0.5511 (mtt) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.0856 time to fit residues: 8.3271 Evaluate side-chains 74 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131717 restraints weight = 6876.857| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.83 r_work: 0.3799 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4710 Z= 0.136 Angle : 0.538 6.724 6433 Z= 0.284 Chirality : 0.039 0.144 679 Planarity : 0.005 0.050 771 Dihedral : 9.007 58.543 786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.55 % Allowed : 15.74 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.38), residues: 501 helix: 1.47 (0.38), residues: 192 sheet: -0.64 (0.47), residues: 114 loop : 0.08 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.012 0.001 TYR B 85 PHE 0.019 0.002 PHE C 59 TRP 0.011 0.001 TRP A 22 HIS 0.006 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4707) covalent geometry : angle 0.53836 / 0.28 ( 6433) hydrogen bonds : bond 0.03629 / 2.53 ( 226) hydrogen bonds : angle 5.12263 / 3.57 ( 676) metal coordination : bond 0.00129 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.167 Fit side-chains REVERT: A 19 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7482 (mmm) REVERT: A 64 ARG cc_start: 0.8339 (ptp-110) cc_final: 0.7716 (ppt170) REVERT: A 81 TRP cc_start: 0.7472 (t-100) cc_final: 0.6968 (t-100) REVERT: A 212 GLU cc_start: 0.8466 (pp20) cc_final: 0.8063 (pp20) REVERT: B 110 TRP cc_start: 0.7929 (t60) cc_final: 0.7576 (t60) REVERT: B 118 ARG cc_start: 0.8558 (mtp-110) cc_final: 0.8171 (mtp-110) REVERT: B 129 GLU cc_start: 0.7809 (pm20) cc_final: 0.7503 (pm20) REVERT: C 66 MET cc_start: 0.5968 (mtp) cc_final: 0.5451 (mtt) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0922 time to fit residues: 8.9300 Evaluate side-chains 75 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128893 restraints weight = 7010.839| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.86 r_work: 0.3760 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4710 Z= 0.192 Angle : 0.581 9.813 6433 Z= 0.305 Chirality : 0.041 0.151 679 Planarity : 0.005 0.053 771 Dihedral : 9.060 58.733 786 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.00 % Allowed : 15.30 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.38), residues: 501 helix: 1.39 (0.38), residues: 191 sheet: -0.82 (0.46), residues: 115 loop : 0.02 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.010 0.002 TYR B 85 PHE 0.018 0.002 PHE C 59 TRP 0.011 0.001 TRP A 73 HIS 0.006 0.002 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 4707) covalent geometry : angle 0.58110 / 0.30 ( 6433) hydrogen bonds : bond 0.03841 / 2.66 ( 226) hydrogen bonds : angle 5.10944 / 3.58 ( 676) metal coordination : bond 0.00299 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.132 Fit side-chains REVERT: A 19 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7455 (mmm) REVERT: A 64 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.7762 (ppt170) REVERT: A 81 TRP cc_start: 0.7604 (t-100) cc_final: 0.7212 (t-100) REVERT: A 212 GLU cc_start: 0.8470 (pp20) cc_final: 0.7967 (pp20) REVERT: B 11 LYS cc_start: 0.7629 (mmtm) cc_final: 0.7304 (mmtm) REVERT: B 110 TRP cc_start: 0.7992 (t60) cc_final: 0.7618 (t60) REVERT: B 118 ARG cc_start: 0.8577 (mtp-110) cc_final: 0.8162 (mtp-110) REVERT: B 129 GLU cc_start: 0.7952 (pm20) cc_final: 0.7620 (pm20) REVERT: C 66 MET cc_start: 0.5975 (mtp) cc_final: 0.5402 (mtt) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.1062 time to fit residues: 10.1563 Evaluate side-chains 77 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 104 ASN B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.152428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.128580 restraints weight = 7037.994| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.83 r_work: 0.3756 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4710 Z= 0.183 Angle : 0.571 8.448 6433 Z= 0.304 Chirality : 0.041 0.153 679 Planarity : 0.005 0.061 771 Dihedral : 9.105 58.831 786 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.00 % Allowed : 16.63 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.37), residues: 501 helix: 1.35 (0.39), residues: 191 sheet: -0.87 (0.46), residues: 113 loop : -0.11 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.012 0.002 TYR A 137 PHE 0.019 0.002 PHE C 59 TRP 0.011 0.002 TRP A 73 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 4707) covalent geometry : angle 0.57124 / 0.30 ( 6433) hydrogen bonds : bond 0.03864 / 2.67 ( 226) hydrogen bonds : angle 5.13320 / 3.58 ( 676) metal coordination : bond 0.00289 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.098 Fit side-chains REVERT: A 19 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7412 (mmm) REVERT: A 64 ARG cc_start: 0.8398 (ptp-110) cc_final: 0.7779 (ppt170) REVERT: A 81 TRP cc_start: 0.7657 (t-100) cc_final: 0.6676 (t-100) REVERT: A 212 GLU cc_start: 0.8420 (pp20) cc_final: 0.7913 (pp20) REVERT: B 7 ASP cc_start: 0.7308 (p0) cc_final: 0.7065 (p0) REVERT: B 11 LYS cc_start: 0.7622 (mmtm) cc_final: 0.7359 (mmtt) REVERT: B 110 TRP cc_start: 0.7978 (t60) cc_final: 0.7550 (t60) REVERT: B 118 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8144 (mtp-110) REVERT: B 129 GLU cc_start: 0.7952 (pm20) cc_final: 0.7615 (pm20) REVERT: C 66 MET cc_start: 0.5963 (mtp) cc_final: 0.5386 (mtt) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.0585 time to fit residues: 5.9032 Evaluate side-chains 77 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 102 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.154145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.130103 restraints weight = 7026.679| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.86 r_work: 0.3773 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4710 Z= 0.135 Angle : 0.558 8.399 6433 Z= 0.292 Chirality : 0.039 0.145 679 Planarity : 0.005 0.053 771 Dihedral : 9.025 58.773 786 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 16.85 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.38), residues: 501 helix: 1.45 (0.38), residues: 191 sheet: -0.69 (0.47), residues: 113 loop : -0.02 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.018 0.001 TYR A 28 PHE 0.020 0.002 PHE C 59 TRP 0.015 0.001 TRP A 22 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4707) covalent geometry : angle 0.55817 / 0.29 ( 6433) hydrogen bonds : bond 0.03673 / 2.56 ( 226) hydrogen bonds : angle 5.05930 / 3.52 ( 676) metal coordination : bond 0.00146 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.096 Fit side-chains REVERT: A 19 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7315 (mmm) REVERT: A 64 ARG cc_start: 0.8390 (ptp-110) cc_final: 0.7762 (ppt170) REVERT: A 81 TRP cc_start: 0.7620 (t-100) cc_final: 0.7390 (t-100) REVERT: A 212 GLU cc_start: 0.8383 (pp20) cc_final: 0.7848 (pp20) REVERT: B 11 LYS cc_start: 0.7581 (mmtm) cc_final: 0.7355 (mmtp) REVERT: B 110 TRP cc_start: 0.7959 (t60) cc_final: 0.7524 (t60) REVERT: B 118 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8158 (mtp-110) REVERT: B 129 GLU cc_start: 0.7916 (pm20) cc_final: 0.7583 (pm20) REVERT: C 66 MET cc_start: 0.6000 (mtp) cc_final: 0.5441 (mtt) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.0684 time to fit residues: 6.7752 Evaluate side-chains 78 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 41 optimal weight: 0.5980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.155196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131337 restraints weight = 6940.578| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.83 r_work: 0.3796 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4710 Z= 0.122 Angle : 0.572 12.031 6433 Z= 0.296 Chirality : 0.039 0.145 679 Planarity : 0.005 0.051 771 Dihedral : 8.930 58.704 786 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.33 % Allowed : 18.63 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.38), residues: 501 helix: 1.48 (0.39), residues: 191 sheet: -0.55 (0.48), residues: 113 loop : 0.02 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.015 0.001 TYR B 85 PHE 0.020 0.002 PHE C 59 TRP 0.014 0.001 TRP A 22 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 4707) covalent geometry : angle 0.57231 / 0.30 ( 6433) hydrogen bonds : bond 0.03568 / 2.49 ( 226) hydrogen bonds : angle 5.01309 / 3.49 ( 676) metal coordination : bond 0.00237 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.155 Fit side-chains REVERT: A 64 ARG cc_start: 0.8352 (ptp-110) cc_final: 0.7753 (ppt170) REVERT: A 81 TRP cc_start: 0.7525 (t-100) cc_final: 0.7316 (t-100) REVERT: A 212 GLU cc_start: 0.8327 (pp20) cc_final: 0.7801 (pp20) REVERT: B 110 TRP cc_start: 0.7923 (t60) cc_final: 0.7546 (t60) REVERT: B 129 GLU cc_start: 0.7933 (pm20) cc_final: 0.7618 (pm20) REVERT: C 66 MET cc_start: 0.5998 (mtp) cc_final: 0.5424 (mtt) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.0885 time to fit residues: 8.4171 Evaluate side-chains 72 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.154569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130729 restraints weight = 6967.294| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.84 r_work: 0.3783 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4710 Z= 0.143 Angle : 0.623 14.544 6433 Z= 0.314 Chirality : 0.040 0.145 679 Planarity : 0.005 0.054 771 Dihedral : 8.909 58.742 786 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.33 % Allowed : 18.18 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.38), residues: 501 helix: 1.35 (0.38), residues: 191 sheet: -0.54 (0.48), residues: 113 loop : -0.04 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 118 TYR 0.013 0.001 TYR B 85 PHE 0.019 0.002 PHE C 59 TRP 0.013 0.001 TRP A 22 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4707) covalent geometry : angle 0.62324 / 0.31 ( 6433) hydrogen bonds : bond 0.03636 / 2.53 ( 226) hydrogen bonds : angle 5.04539 / 3.52 ( 676) metal coordination : bond 0.00261 / 0.13 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.167 Fit side-chains REVERT: A 64 ARG cc_start: 0.8371 (ptp-110) cc_final: 0.7771 (ppt170) REVERT: A 212 GLU cc_start: 0.8286 (pp20) cc_final: 0.7760 (pp20) REVERT: B 110 TRP cc_start: 0.7953 (t60) cc_final: 0.7569 (t60) REVERT: B 129 GLU cc_start: 0.7949 (pm20) cc_final: 0.7622 (pm20) REVERT: C 66 MET cc_start: 0.6021 (mtp) cc_final: 0.5427 (mtt) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.0879 time to fit residues: 8.0839 Evaluate side-chains 73 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 48 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** 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 = 0.4210 r_free = 0.4210 target = 0.153555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130623 restraints weight = 7119.802| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.70 r_work: 0.3771 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4710 Z= 0.176 Angle : 0.632 11.802 6433 Z= 0.321 Chirality : 0.041 0.147 679 Planarity : 0.005 0.061 771 Dihedral : 8.969 58.841 786 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.11 % Allowed : 18.85 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.37), residues: 501 helix: 1.27 (0.38), residues: 191 sheet: -0.69 (0.47), residues: 113 loop : -0.16 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.014 0.002 TYR B 85 PHE 0.018 0.002 PHE C 59 TRP 0.012 0.002 TRP A 73 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 4707) covalent geometry : angle 0.63204 / 0.32 ( 6433) hydrogen bonds : bond 0.03797 / 2.63 ( 226) hydrogen bonds : angle 5.10786 / 3.58 ( 676) metal coordination : bond 0.00405 / 0.21 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1189.07 seconds wall clock time: 21 minutes 11.44 seconds (1271.44 seconds total)