Starting phenix.real_space_refine on Tue Mar 3 12:35:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.map" model { file = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2026/6y97_10733.cif" } resolution = 4.33 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= 0.026 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 36 5.16 5 C 2840 2.51 5 N 700 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 1.18, per 1000 atoms: 0.27 Number of scatterers: 4366 At special positions: 0 Unit cell: (61.05, 65.934, 118.03, 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 36 16.00 O 790 8.00 N 700 7.00 C 2840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 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: 0.39 Conformation dependent library (CDL) restraints added in 181.7 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.3% alpha, 11.5% 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 50 through 70 removed outlier: 4.157A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.626A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.955A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 143 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 213 removed outlier: 4.121A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.880A pdb=" N SER B 49 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.855A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.301A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.521A pdb=" N LYS B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.617A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.510A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.177A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.646A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.056A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN L 50 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 42 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 609 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: 0.58 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: 1.23 - 1.35: 1335 1.35 - 1.46: 1057 1.46 - 1.58: 2016 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 4468 Sorted by residual: bond pdb=" N GLN L 55 " pdb=" CA GLN L 55 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 bond pdb=" CB PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.23e+00 bond pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.07e-01 bond pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5971 2.11 - 4.21: 72 4.21 - 6.32: 8 6.32 - 8.43: 3 8.43 - 10.53: 1 Bond angle restraints: 6055 Sorted by residual: angle pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C GLN L 43 " pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 121.95 111.42 10.53 3.74e+00 7.15e-02 7.93e+00 angle pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " pdb=" CG GLN L 55 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.61e+00 angle pdb=" CA LYS B 50 " pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C GLN L 55 " pdb=" N MET L 56 " pdb=" CA MET L 56 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 6050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2369 17.99 - 35.98: 227 35.98 - 53.97: 46 53.97 - 71.96: 5 71.96 - 89.95: 5 Dihedral angle restraints: 2652 sinusoidal: 1031 harmonic: 1621 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 55.10 37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB MET A 93 " pdb=" CG MET A 93 " pdb=" SD MET A 93 " pdb=" CE MET A 93 " ideal model delta sinusoidal sigma weight residual -60.00 -113.09 53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CB MET A 136 " pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sinusoidal sigma weight residual 180.00 127.86 52.14 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 461 0.034 - 0.069: 154 0.069 - 0.103: 60 0.103 - 0.137: 12 0.137 - 0.172: 1 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE L 53 " pdb=" N ILE L 53 " pdb=" C ILE L 53 " pdb=" CB ILE L 53 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 685 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 78 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO B 79 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 63 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO L 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 9.89e-03 1.96e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 80 2.70 - 3.25: 4316 3.25 - 3.80: 6674 3.80 - 4.35: 7774 4.35 - 4.90: 13128 Nonbonded interactions: 31972 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OG SER H 30 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" O ALA A 126 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O ASN B 163 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR H 69 " pdb=" O GLU H 82 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASN A 171 " pdb=" OG SER A 173 " model vdw 2.271 3.040 ... (remaining 31967 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 group one per residue 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: 3.560 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.490 Find NCS groups from input model: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 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 : 0.002 0.055 4472 Z= 0.115 Angle : 0.578 10.533 6063 Z= 0.293 Chirality : 0.040 0.172 688 Planarity : 0.005 0.098 748 Dihedral : 14.610 89.950 1608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.38), residues: 556 helix: 2.81 (0.36), residues: 210 sheet: 0.41 (0.53), residues: 92 loop : -1.00 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 66 TYR 0.024 0.001 TYR A 94 PHE 0.015 0.001 PHE B 146 TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4468) covalent geometry : angle 0.57797 ( 6055) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.33322 ( 8) hydrogen bonds : bond 0.16067 ( 216) hydrogen bonds : angle 5.18148 ( 609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8965 (tmmt) REVERT: B 163 ASN cc_start: 0.6919 (t0) cc_final: 0.6610 (t0) REVERT: H 46 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7360 (tm-30) REVERT: H 48 MET cc_start: 0.6952 (ppp) cc_final: 0.6251 (ppp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0587 time to fit residues: 12.5799 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 181 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126486 restraints weight = 11507.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.130417 restraints weight = 7635.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.133407 restraints weight = 5421.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.135605 restraints weight = 4025.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137257 restraints weight = 3110.515| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4472 Z= 0.116 Angle : 0.559 6.836 6063 Z= 0.280 Chirality : 0.041 0.137 688 Planarity : 0.005 0.063 748 Dihedral : 3.638 13.978 603 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.21 % Allowed : 4.57 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.38), residues: 556 helix: 2.68 (0.35), residues: 225 sheet: 0.65 (0.51), residues: 99 loop : -1.06 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.021 0.001 TYR A 94 PHE 0.036 0.002 PHE A 62 TRP 0.012 0.001 TRP B 89 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4468) covalent geometry : angle 0.55729 ( 6055) SS BOND : bond 0.00990 ( 4) SS BOND : angle 1.19263 ( 8) hydrogen bonds : bond 0.03599 ( 216) hydrogen bonds : angle 3.94874 ( 609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8469 (pp) cc_final: 0.8109 (tt) REVERT: A 187 GLN cc_start: 0.8689 (mt0) cc_final: 0.8410 (mt0) REVERT: B 50 LYS cc_start: 0.9257 (tmtt) cc_final: 0.9003 (tmmt) REVERT: B 163 ASN cc_start: 0.7896 (t0) cc_final: 0.7683 (t0) REVERT: H 13 LYS cc_start: 0.7148 (tppt) cc_final: 0.6922 (mmmt) REVERT: H 27 TYR cc_start: 0.8453 (p90) cc_final: 0.8122 (p90) REVERT: H 46 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7863 (tm-30) REVERT: H 47 TRP cc_start: 0.9036 (t60) cc_final: 0.8243 (t60) REVERT: H 48 MET cc_start: 0.8195 (ppp) cc_final: 0.7560 (ppp) REVERT: H 90 ASP cc_start: 0.8567 (m-30) cc_final: 0.8269 (m-30) REVERT: L 42 LEU cc_start: 0.8907 (mm) cc_final: 0.8451 (mm) REVERT: L 107 THR cc_start: 0.7580 (p) cc_final: 0.7341 (p) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.0537 time to fit residues: 11.0498 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 181 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.133401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113117 restraints weight = 11393.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116791 restraints weight = 7382.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119472 restraints weight = 5187.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.121522 restraints weight = 3850.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.123114 restraints weight = 2967.286| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4472 Z= 0.185 Angle : 0.653 10.888 6063 Z= 0.333 Chirality : 0.043 0.142 688 Planarity : 0.005 0.053 748 Dihedral : 4.326 18.234 603 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.99 (0.37), residues: 556 helix: 2.41 (0.34), residues: 226 sheet: 0.97 (0.53), residues: 85 loop : -1.22 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 82 TYR 0.029 0.002 TYR A 94 PHE 0.017 0.002 PHE B 146 TRP 0.015 0.002 TRP B 89 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 4468) covalent geometry : angle 0.65164 ( 6055) SS BOND : bond 0.00842 ( 4) SS BOND : angle 1.31194 ( 8) hydrogen bonds : bond 0.04037 ( 216) hydrogen bonds : angle 4.14069 ( 609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8776 (pp) cc_final: 0.8339 (tt) REVERT: A 166 ASN cc_start: 0.8729 (t0) cc_final: 0.7867 (m-40) REVERT: A 187 GLN cc_start: 0.8778 (mt0) cc_final: 0.8489 (mt0) REVERT: A 205 GLU cc_start: 0.8157 (pt0) cc_final: 0.7901 (pt0) REVERT: B 48 GLU cc_start: 0.9024 (tp30) cc_final: 0.8799 (pm20) REVERT: B 50 LYS cc_start: 0.9394 (tmtt) cc_final: 0.9105 (tmmt) REVERT: B 59 ASN cc_start: 0.8290 (m110) cc_final: 0.7823 (m110) REVERT: H 13 LYS cc_start: 0.7325 (tppt) cc_final: 0.7032 (mmmt) REVERT: H 47 TRP cc_start: 0.9061 (t60) cc_final: 0.8442 (t60) REVERT: H 48 MET cc_start: 0.8191 (ppp) cc_final: 0.7414 (ppp) REVERT: H 57 ASP cc_start: 0.8743 (t0) cc_final: 0.8514 (t0) REVERT: H 81 MET cc_start: 0.3860 (tpt) cc_final: 0.3555 (tpt) REVERT: H 90 ASP cc_start: 0.8877 (m-30) cc_final: 0.8601 (m-30) REVERT: L 42 LEU cc_start: 0.9108 (mm) cc_final: 0.8851 (mm) REVERT: L 107 THR cc_start: 0.8297 (p) cc_final: 0.8073 (p) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0569 time to fit residues: 11.6757 Evaluate side-chains 128 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN H 6 GLN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.137659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.116238 restraints weight = 11233.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.120086 restraints weight = 7249.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122917 restraints weight = 5042.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.125061 restraints weight = 3706.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126602 restraints weight = 2829.608| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4472 Z= 0.116 Angle : 0.604 7.321 6063 Z= 0.301 Chirality : 0.042 0.132 688 Planarity : 0.004 0.047 748 Dihedral : 4.149 16.417 603 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.37), residues: 556 helix: 2.55 (0.34), residues: 225 sheet: 0.92 (0.52), residues: 88 loop : -1.21 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.030 0.002 TYR A 94 PHE 0.017 0.002 PHE L 67 TRP 0.015 0.001 TRP B 89 HIS 0.001 0.000 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4468) covalent geometry : angle 0.60345 ( 6055) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.01333 ( 8) hydrogen bonds : bond 0.03627 ( 216) hydrogen bonds : angle 3.68641 ( 609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8766 (pp) cc_final: 0.8358 (tt) REVERT: A 166 ASN cc_start: 0.8620 (t0) cc_final: 0.7867 (m-40) REVERT: A 174 GLU cc_start: 0.9168 (mp0) cc_final: 0.8590 (mp0) REVERT: A 183 CYS cc_start: 0.7665 (p) cc_final: 0.7414 (p) REVERT: A 187 GLN cc_start: 0.8720 (mt0) cc_final: 0.8348 (mt0) REVERT: B 48 GLU cc_start: 0.9120 (tp30) cc_final: 0.8739 (pm20) REVERT: B 50 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9067 (tmmt) REVERT: B 59 ASN cc_start: 0.8316 (m110) cc_final: 0.7845 (m110) REVERT: H 13 LYS cc_start: 0.7157 (tppt) cc_final: 0.6828 (mmmt) REVERT: H 19 LYS cc_start: 0.8680 (mppt) cc_final: 0.8209 (tppp) REVERT: H 46 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7532 (tm-30) REVERT: H 47 TRP cc_start: 0.8987 (t60) cc_final: 0.8415 (t60) REVERT: H 48 MET cc_start: 0.8182 (ppp) cc_final: 0.7397 (ppp) REVERT: H 57 ASP cc_start: 0.8754 (t0) cc_final: 0.8458 (t0) REVERT: H 90 ASP cc_start: 0.8881 (m-30) cc_final: 0.8590 (m-30) REVERT: H 102 ASP cc_start: 0.8195 (t70) cc_final: 0.7894 (t0) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.0543 time to fit residues: 11.5075 Evaluate side-chains 139 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.126806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106231 restraints weight = 11518.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.109952 restraints weight = 7304.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112672 restraints weight = 5045.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114696 restraints weight = 3688.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116174 restraints weight = 2798.399| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4472 Z= 0.176 Angle : 0.668 7.630 6063 Z= 0.341 Chirality : 0.043 0.144 688 Planarity : 0.005 0.049 748 Dihedral : 4.719 20.316 603 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.75 (0.37), residues: 556 helix: 2.28 (0.34), residues: 225 sheet: 0.70 (0.51), residues: 88 loop : -1.38 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 50 TYR 0.025 0.002 TYR A 94 PHE 0.034 0.003 PHE B 62 TRP 0.018 0.002 TRP H 33 HIS 0.009 0.002 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4468) covalent geometry : angle 0.66720 ( 6055) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.23546 ( 8) hydrogen bonds : bond 0.03944 ( 216) hydrogen bonds : angle 4.00696 ( 609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9145 (m110) cc_final: 0.8923 (m110) REVERT: A 133 LEU cc_start: 0.8914 (pp) cc_final: 0.8596 (tt) REVERT: A 174 GLU cc_start: 0.9197 (mp0) cc_final: 0.8601 (mp0) REVERT: A 187 GLN cc_start: 0.8801 (mt0) cc_final: 0.8467 (mt0) REVERT: A 205 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8683 (tm-30) REVERT: B 50 LYS cc_start: 0.9469 (tmtt) cc_final: 0.9112 (tmmt) REVERT: B 124 LEU cc_start: 0.9457 (mm) cc_final: 0.9235 (mm) REVERT: B 148 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8293 (pttt) REVERT: H 13 LYS cc_start: 0.7440 (tppt) cc_final: 0.7070 (mmmt) REVERT: H 46 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7446 (tm-30) REVERT: H 47 TRP cc_start: 0.8987 (t60) cc_final: 0.8372 (t60) REVERT: H 48 MET cc_start: 0.8297 (ppp) cc_final: 0.7616 (ppp) REVERT: H 57 ASP cc_start: 0.8764 (t0) cc_final: 0.8340 (t0) REVERT: H 90 ASP cc_start: 0.9038 (m-30) cc_final: 0.8714 (m-30) REVERT: H 102 ASP cc_start: 0.8330 (t70) cc_final: 0.7990 (t70) REVERT: L 4 MET cc_start: 0.8710 (mpp) cc_final: 0.8323 (mpp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0569 time to fit residues: 11.9375 Evaluate side-chains 138 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 56 GLN B 140 ASN B 145 HIS B 158 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.134382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113328 restraints weight = 11937.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117166 restraints weight = 7684.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.119923 restraints weight = 5332.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.121933 restraints weight = 3901.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.123426 restraints weight = 2979.942| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4472 Z= 0.121 Angle : 0.635 7.782 6063 Z= 0.315 Chirality : 0.043 0.133 688 Planarity : 0.005 0.049 748 Dihedral : 4.397 15.419 603 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.87 (0.37), residues: 556 helix: 2.40 (0.34), residues: 225 sheet: 0.71 (0.53), residues: 88 loop : -1.31 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 50 TYR 0.030 0.002 TYR A 94 PHE 0.015 0.002 PHE B 146 TRP 0.015 0.002 TRP B 89 HIS 0.010 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4468) covalent geometry : angle 0.63487 ( 6055) SS BOND : bond 0.00715 ( 4) SS BOND : angle 0.76856 ( 8) hydrogen bonds : bond 0.03544 ( 216) hydrogen bonds : angle 3.65498 ( 609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8815 (m110) cc_final: 0.8575 (m110) REVERT: A 133 LEU cc_start: 0.8924 (pp) cc_final: 0.8583 (tt) REVERT: A 166 ASN cc_start: 0.8708 (t0) cc_final: 0.8008 (m-40) REVERT: A 174 GLU cc_start: 0.9209 (mp0) cc_final: 0.8734 (mp0) REVERT: A 187 GLN cc_start: 0.8731 (mt0) cc_final: 0.8429 (mt0) REVERT: A 205 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8648 (tm-30) REVERT: B 50 LYS cc_start: 0.9424 (tmtt) cc_final: 0.9082 (tmmt) REVERT: B 59 ASN cc_start: 0.8122 (t0) cc_final: 0.7899 (m110) REVERT: H 13 LYS cc_start: 0.7357 (tppt) cc_final: 0.6999 (mmmt) REVERT: H 46 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7436 (tm-30) REVERT: H 47 TRP cc_start: 0.8973 (t60) cc_final: 0.8381 (t60) REVERT: H 48 MET cc_start: 0.8147 (ppp) cc_final: 0.7662 (ppp) REVERT: H 57 ASP cc_start: 0.8720 (t0) cc_final: 0.8310 (t0) REVERT: H 68 VAL cc_start: 0.8007 (t) cc_final: 0.7225 (t) REVERT: H 81 MET cc_start: 0.4440 (tpt) cc_final: 0.4170 (tpp) REVERT: H 90 ASP cc_start: 0.8965 (m-30) cc_final: 0.8671 (m-30) REVERT: H 102 ASP cc_start: 0.8408 (t70) cc_final: 0.7957 (t0) REVERT: L 4 MET cc_start: 0.8661 (mpp) cc_final: 0.8282 (mpp) REVERT: L 98 GLU cc_start: 0.8421 (pt0) cc_final: 0.8181 (mp0) REVERT: L 107 THR cc_start: 0.8508 (p) cc_final: 0.8221 (p) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0550 time to fit residues: 11.7425 Evaluate side-chains 138 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 158 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.128881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108387 restraints weight = 11923.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.112020 restraints weight = 7609.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114651 restraints weight = 5288.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116602 restraints weight = 3900.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.117835 restraints weight = 2995.151| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4472 Z= 0.141 Angle : 0.643 7.859 6063 Z= 0.322 Chirality : 0.043 0.147 688 Planarity : 0.005 0.048 748 Dihedral : 4.512 17.872 603 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.78 (0.37), residues: 556 helix: 2.37 (0.34), residues: 225 sheet: 0.54 (0.51), residues: 88 loop : -1.36 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 50 TYR 0.027 0.002 TYR A 94 PHE 0.039 0.002 PHE A 62 TRP 0.020 0.002 TRP H 33 HIS 0.006 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4468) covalent geometry : angle 0.64246 ( 6055) SS BOND : bond 0.00424 ( 4) SS BOND : angle 1.04412 ( 8) hydrogen bonds : bond 0.03630 ( 216) hydrogen bonds : angle 3.77435 ( 609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9104 (m110) cc_final: 0.8833 (m110) REVERT: A 166 ASN cc_start: 0.8802 (t0) cc_final: 0.8168 (m-40) REVERT: A 171 ASN cc_start: 0.8789 (p0) cc_final: 0.8102 (p0) REVERT: A 174 GLU cc_start: 0.9145 (mp0) cc_final: 0.8774 (mp0) REVERT: A 187 GLN cc_start: 0.8764 (mt0) cc_final: 0.8461 (mt0) REVERT: A 205 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 50 LYS cc_start: 0.9460 (tmtt) cc_final: 0.9161 (tmmt) REVERT: B 59 ASN cc_start: 0.8819 (t0) cc_final: 0.8298 (m-40) REVERT: B 148 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8227 (pttt) REVERT: H 46 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7420 (tm-30) REVERT: H 47 TRP cc_start: 0.8981 (t60) cc_final: 0.8365 (t60) REVERT: H 48 MET cc_start: 0.8295 (ppp) cc_final: 0.7687 (ppp) REVERT: H 57 ASP cc_start: 0.8739 (t0) cc_final: 0.8398 (t0) REVERT: H 68 VAL cc_start: 0.8142 (t) cc_final: 0.7421 (t) REVERT: H 81 MET cc_start: 0.4700 (tpt) cc_final: 0.4379 (tpp) REVERT: H 90 ASP cc_start: 0.9064 (m-30) cc_final: 0.8746 (m-30) REVERT: H 102 ASP cc_start: 0.8398 (t70) cc_final: 0.7945 (t70) REVERT: L 107 THR cc_start: 0.8602 (p) cc_final: 0.8281 (p) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0563 time to fit residues: 11.9427 Evaluate side-chains 139 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.0270 chunk 36 optimal weight: 0.0770 chunk 13 optimal weight: 0.0070 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 140 ASN B 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.133206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112390 restraints weight = 11569.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.116253 restraints weight = 7294.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.119008 restraints weight = 5022.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.120967 restraints weight = 3677.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122521 restraints weight = 2827.514| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4472 Z= 0.117 Angle : 0.643 7.161 6063 Z= 0.319 Chirality : 0.043 0.148 688 Planarity : 0.005 0.049 748 Dihedral : 4.341 15.606 603 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.91 (0.38), residues: 556 helix: 2.44 (0.35), residues: 224 sheet: 0.63 (0.51), residues: 98 loop : -1.33 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.030 0.002 TYR A 94 PHE 0.034 0.002 PHE A 62 TRP 0.019 0.002 TRP H 109 HIS 0.002 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4468) covalent geometry : angle 0.64245 ( 6055) SS BOND : bond 0.00366 ( 4) SS BOND : angle 0.72008 ( 8) hydrogen bonds : bond 0.03515 ( 216) hydrogen bonds : angle 3.59171 ( 609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9095 (m110) cc_final: 0.8864 (m110) REVERT: A 71 MET cc_start: 0.8929 (mmt) cc_final: 0.8728 (mmm) REVERT: A 166 ASN cc_start: 0.8714 (t0) cc_final: 0.8133 (m-40) REVERT: A 171 ASN cc_start: 0.8782 (p0) cc_final: 0.8174 (p0) REVERT: A 174 GLU cc_start: 0.9138 (mp0) cc_final: 0.8850 (mp0) REVERT: A 187 GLN cc_start: 0.8768 (mt0) cc_final: 0.8475 (mt0) REVERT: A 202 PHE cc_start: 0.7959 (t80) cc_final: 0.7731 (t80) REVERT: A 205 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8622 (tm-30) REVERT: B 50 LYS cc_start: 0.9442 (tmtt) cc_final: 0.9121 (tmmt) REVERT: B 59 ASN cc_start: 0.8411 (t0) cc_final: 0.8040 (m110) REVERT: H 13 LYS cc_start: 0.7279 (tppt) cc_final: 0.6951 (mmmt) REVERT: H 46 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7341 (tm-30) REVERT: H 47 TRP cc_start: 0.8970 (t60) cc_final: 0.8305 (t60) REVERT: H 48 MET cc_start: 0.8195 (ppp) cc_final: 0.7663 (ppp) REVERT: H 57 ASP cc_start: 0.8753 (t0) cc_final: 0.8399 (t0) REVERT: H 81 MET cc_start: 0.4607 (tpt) cc_final: 0.4324 (tpp) REVERT: H 90 ASP cc_start: 0.8957 (m-30) cc_final: 0.8636 (m-30) REVERT: H 102 ASP cc_start: 0.8437 (t70) cc_final: 0.7905 (t70) REVERT: L 98 GLU cc_start: 0.8417 (pt0) cc_final: 0.8170 (mp0) REVERT: L 102 THR cc_start: 0.8017 (m) cc_final: 0.7687 (m) REVERT: L 107 THR cc_start: 0.8548 (p) cc_final: 0.8184 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0534 time to fit residues: 11.6975 Evaluate side-chains 137 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS H 39 GLN L 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.122051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102720 restraints weight = 12287.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106403 restraints weight = 7584.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108993 restraints weight = 5146.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.110899 restraints weight = 3716.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.112368 restraints weight = 2814.094| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4472 Z= 0.195 Angle : 0.750 10.050 6063 Z= 0.383 Chirality : 0.045 0.164 688 Planarity : 0.005 0.050 748 Dihedral : 4.966 21.276 603 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.21 % Allowed : 0.83 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.50 (0.36), residues: 556 helix: 2.20 (0.35), residues: 218 sheet: 0.22 (0.51), residues: 88 loop : -1.41 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 50 TYR 0.031 0.002 TYR A 94 PHE 0.037 0.003 PHE A 62 TRP 0.029 0.003 TRP H 33 HIS 0.004 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 4468) covalent geometry : angle 0.74945 ( 6055) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.32269 ( 8) hydrogen bonds : bond 0.04184 ( 216) hydrogen bonds : angle 4.12402 ( 609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9354 (m110) cc_final: 0.8823 (m-40) REVERT: A 71 MET cc_start: 0.9186 (mmt) cc_final: 0.8978 (mmt) REVERT: A 166 ASN cc_start: 0.8984 (t0) cc_final: 0.8680 (t0) REVERT: A 171 ASN cc_start: 0.8821 (p0) cc_final: 0.8100 (p0) REVERT: A 174 GLU cc_start: 0.9281 (mp0) cc_final: 0.8839 (mp0) REVERT: A 187 GLN cc_start: 0.8778 (mt0) cc_final: 0.8495 (mt0) REVERT: A 205 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8714 (tm-30) REVERT: B 50 LYS cc_start: 0.9468 (tmtt) cc_final: 0.9149 (tmmt) REVERT: B 59 ASN cc_start: 0.8690 (t0) cc_final: 0.8294 (t0) REVERT: B 117 MET cc_start: 0.6354 (mmm) cc_final: 0.5667 (mtm) REVERT: B 148 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8314 (pttt) REVERT: B 154 PHE cc_start: 0.9117 (p90) cc_final: 0.8909 (p90) REVERT: H 46 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7518 (tm-30) REVERT: H 47 TRP cc_start: 0.9013 (t60) cc_final: 0.8451 (t60) REVERT: H 48 MET cc_start: 0.8429 (ppp) cc_final: 0.7719 (ppp) REVERT: H 57 ASP cc_start: 0.8750 (t0) cc_final: 0.8381 (t0) REVERT: H 90 ASP cc_start: 0.9106 (m-30) cc_final: 0.8894 (m-30) REVERT: H 102 ASP cc_start: 0.8400 (t70) cc_final: 0.7908 (t70) REVERT: L 40 TRP cc_start: 0.8170 (m100) cc_final: 0.7957 (m100) REVERT: L 98 GLU cc_start: 0.8567 (pt0) cc_final: 0.8311 (mp0) REVERT: L 102 THR cc_start: 0.8263 (m) cc_final: 0.7935 (m) REVERT: L 107 THR cc_start: 0.8759 (p) cc_final: 0.8533 (p) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.0520 time to fit residues: 10.9718 Evaluate side-chains 139 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 HIS B 158 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106424 restraints weight = 12004.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110095 restraints weight = 7379.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112780 restraints weight = 5010.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114665 restraints weight = 3619.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116166 restraints weight = 2752.084| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4472 Z= 0.136 Angle : 0.685 8.893 6063 Z= 0.341 Chirality : 0.043 0.158 688 Planarity : 0.005 0.050 748 Dihedral : 4.706 17.954 603 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.37), residues: 556 helix: 2.31 (0.35), residues: 218 sheet: 0.33 (0.50), residues: 98 loop : -1.39 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 50 TYR 0.031 0.002 TYR A 94 PHE 0.029 0.002 PHE A 62 TRP 0.017 0.002 TRP H 33 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4468) covalent geometry : angle 0.68484 ( 6055) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.97514 ( 8) hydrogen bonds : bond 0.03715 ( 216) hydrogen bonds : angle 3.92049 ( 609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 VAL cc_start: 0.9321 (t) cc_final: 0.8873 (t) REVERT: A 59 ASN cc_start: 0.9051 (m110) cc_final: 0.8178 (m110) REVERT: A 166 ASN cc_start: 0.8843 (t0) cc_final: 0.8267 (m110) REVERT: A 171 ASN cc_start: 0.8694 (p0) cc_final: 0.7978 (p0) REVERT: A 174 GLU cc_start: 0.9248 (mp0) cc_final: 0.8858 (mp0) REVERT: A 187 GLN cc_start: 0.8753 (mt0) cc_final: 0.8290 (mt0) REVERT: A 205 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8672 (tm-30) REVERT: B 50 LYS cc_start: 0.9494 (tmtt) cc_final: 0.9134 (tmmt) REVERT: B 117 MET cc_start: 0.6217 (mmm) cc_final: 0.5494 (mtm) REVERT: B 154 PHE cc_start: 0.9101 (p90) cc_final: 0.8899 (p90) REVERT: H 46 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 47 TRP cc_start: 0.9006 (t60) cc_final: 0.8412 (t60) REVERT: H 48 MET cc_start: 0.8374 (ppp) cc_final: 0.7679 (ppp) REVERT: H 57 ASP cc_start: 0.8734 (t0) cc_final: 0.8387 (t0) REVERT: H 81 MET cc_start: 0.4669 (tpt) cc_final: 0.4444 (tpp) REVERT: H 90 ASP cc_start: 0.9076 (m-30) cc_final: 0.8865 (m-30) REVERT: H 102 ASP cc_start: 0.8453 (t70) cc_final: 0.7879 (t70) REVERT: L 102 THR cc_start: 0.8093 (m) cc_final: 0.7625 (m) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0564 time to fit residues: 12.5701 Evaluate side-chains 147 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.0000 chunk 18 optimal weight: 0.7980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108440 restraints weight = 11901.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112094 restraints weight = 7364.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114785 restraints weight = 4999.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116666 restraints weight = 3595.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118096 restraints weight = 2721.737| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4472 Z= 0.131 Angle : 0.704 8.349 6063 Z= 0.350 Chirality : 0.044 0.160 688 Planarity : 0.005 0.053 748 Dihedral : 4.612 16.040 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.51 (0.37), residues: 556 helix: 2.04 (0.34), residues: 217 sheet: 0.43 (0.51), residues: 98 loop : -1.34 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 50 TYR 0.032 0.002 TYR A 94 PHE 0.016 0.002 PHE B 62 TRP 0.024 0.002 TRP H 109 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4468) covalent geometry : angle 0.70366 ( 6055) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.86573 ( 8) hydrogen bonds : bond 0.03740 ( 216) hydrogen bonds : angle 3.89603 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.77 seconds wall clock time: 17 minutes 8.00 seconds (1028.00 seconds total)