Starting phenix.real_space_refine on Tue Feb 11 06:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y97_10733/02_2025/6y97_10733.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y97_10733/02_2025/6y97_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_10733/02_2025/6y97_10733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y97_10733/02_2025/6y97_10733.map" model { file = "/net/cci-nas-00/data/ceres_data/6y97_10733/02_2025/6y97_10733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y97_10733/02_2025/6y97_10733.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.43, per 1000 atoms: 0.79 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: 1.14 Conformation dependent library (CDL) restraints added in 556.1 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: 0.48 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: 1.07 Time building geometry restraints manager: 1.32 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- 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 4468 Z= 0.163 Angle : 0.578 10.533 6055 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (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 TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS A 63 PHE 0.015 0.001 PHE B 146 TYR 0.024 0.001 TYR A 94 ARG 0.003 0.000 ARG L 66 *********************** 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 : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8963 (tmmt) REVERT: B 163 ASN cc_start: 0.6919 (t0) cc_final: 0.6613 (t0) REVERT: H 46 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7361 (tm-30) REVERT: H 48 MET cc_start: 0.6951 (ppp) cc_final: 0.6250 (ppp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1353 time to fit residues: 28.4952 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 : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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 = 0.4066 r_free = 0.4066 target = 0.138169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117214 restraints weight = 11520.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120993 restraints weight = 7587.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123700 restraints weight = 5320.996| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4468 Z= 0.254 Angle : 0.634 6.848 6055 Z= 0.327 Chirality : 0.043 0.146 688 Planarity : 0.005 0.056 748 Dihedral : 4.281 18.140 603 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.21 % Allowed : 7.07 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.37), residues: 556 helix: 2.23 (0.34), residues: 226 sheet: 0.89 (0.53), residues: 90 loop : -1.19 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.004 0.001 HIS B 63 PHE 0.035 0.003 PHE A 62 TYR 0.028 0.002 TYR A 94 ARG 0.008 0.001 ARG H 50 *********************** 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 155 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8749 (pp) cc_final: 0.8336 (tt) REVERT: A 166 ASN cc_start: 0.8736 (t0) cc_final: 0.8491 (t0) REVERT: A 187 GLN cc_start: 0.8766 (mt0) cc_final: 0.8451 (mt0) REVERT: B 50 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9064 (tmmt) REVERT: B 124 LEU cc_start: 0.9509 (mm) cc_final: 0.9254 (mt) REVERT: H 27 TYR cc_start: 0.8602 (p90) cc_final: 0.8229 (p90) REVERT: H 46 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7536 (tm-30) REVERT: H 47 TRP cc_start: 0.9098 (t60) cc_final: 0.8414 (t60) REVERT: H 48 MET cc_start: 0.8337 (ppp) cc_final: 0.7724 (ppp) REVERT: H 57 ASP cc_start: 0.8957 (t0) cc_final: 0.8695 (t0) REVERT: H 81 MET cc_start: 0.3702 (tpt) cc_final: 0.2975 (tpt) REVERT: H 90 ASP cc_start: 0.8791 (m-30) cc_final: 0.8435 (m-30) REVERT: L 42 LEU cc_start: 0.9012 (mm) cc_final: 0.8793 (mm) REVERT: L 107 THR cc_start: 0.8137 (p) cc_final: 0.7912 (p) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1333 time to fit residues: 26.7854 Evaluate side-chains 130 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.137035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116120 restraints weight = 11502.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119921 restraints weight = 7494.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122776 restraints weight = 5245.346| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4468 Z= 0.189 Angle : 0.596 6.502 6055 Z= 0.303 Chirality : 0.041 0.133 688 Planarity : 0.005 0.050 748 Dihedral : 4.096 17.720 603 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.21 % Allowed : 4.16 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.38), residues: 556 helix: 2.60 (0.34), residues: 225 sheet: 0.78 (0.53), residues: 88 loop : -1.20 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.002 0.001 HIS A 63 PHE 0.021 0.002 PHE A 62 TYR 0.040 0.002 TYR A 94 ARG 0.006 0.001 ARG H 50 *********************** 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: 1 poor density : 153 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8825 (pp) cc_final: 0.8388 (tt) REVERT: A 166 ASN cc_start: 0.8584 (t0) cc_final: 0.8287 (t0) REVERT: A 187 GLN cc_start: 0.8851 (mt0) cc_final: 0.8587 (mt0) REVERT: B 50 LYS cc_start: 0.9387 (tmtt) cc_final: 0.9096 (tmmt) REVERT: B 71 MET cc_start: 0.5705 (ptp) cc_final: 0.5392 (ptp) REVERT: H 13 LYS cc_start: 0.7313 (tppt) cc_final: 0.6992 (mmmt) REVERT: H 47 TRP cc_start: 0.9064 (t60) cc_final: 0.8436 (t60) REVERT: H 48 MET cc_start: 0.8160 (ppp) cc_final: 0.7422 (ppp) REVERT: H 57 ASP cc_start: 0.8931 (t0) cc_final: 0.8620 (t0) REVERT: H 90 ASP cc_start: 0.8844 (m-30) cc_final: 0.8530 (m-30) REVERT: L 18 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.8276 (Cg_endo) REVERT: L 42 LEU cc_start: 0.9400 (mm) cc_final: 0.9099 (mm) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.1336 time to fit residues: 26.6629 Evaluate side-chains 132 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.132315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111674 restraints weight = 11489.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115543 restraints weight = 7408.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118375 restraints weight = 5121.608| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4468 Z= 0.206 Angle : 0.595 6.434 6055 Z= 0.305 Chirality : 0.042 0.134 688 Planarity : 0.005 0.045 748 Dihedral : 4.277 17.664 603 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.37), residues: 556 helix: 2.61 (0.35), residues: 225 sheet: 0.80 (0.52), residues: 88 loop : -1.34 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 89 HIS 0.001 0.000 HIS L 31 PHE 0.017 0.002 PHE A 200 TYR 0.025 0.002 TYR A 94 ARG 0.006 0.001 ARG H 50 *********************** 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 154 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8858 (m110) cc_final: 0.8558 (m110) REVERT: A 133 LEU cc_start: 0.8936 (pp) cc_final: 0.8535 (tt) REVERT: A 166 ASN cc_start: 0.8794 (t0) cc_final: 0.7943 (m110) REVERT: A 174 GLU cc_start: 0.9132 (mp0) cc_final: 0.8586 (mp0) REVERT: A 183 CYS cc_start: 0.7563 (p) cc_final: 0.7358 (p) REVERT: A 187 GLN cc_start: 0.8811 (mt0) cc_final: 0.8558 (mt0) REVERT: B 50 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9114 (tmmt) REVERT: B 71 MET cc_start: 0.5823 (ptp) cc_final: 0.5575 (ptp) REVERT: H 13 LYS cc_start: 0.7225 (tppt) cc_final: 0.6857 (mmmt) REVERT: H 46 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7507 (tm-30) REVERT: H 47 TRP cc_start: 0.8989 (t60) cc_final: 0.8487 (t60) REVERT: H 48 MET cc_start: 0.8282 (ppp) cc_final: 0.7568 (ppp) REVERT: H 57 ASP cc_start: 0.8891 (t0) cc_final: 0.8596 (t0) REVERT: H 90 ASP cc_start: 0.8922 (m-30) cc_final: 0.8616 (m-30) REVERT: H 102 ASP cc_start: 0.8366 (t70) cc_final: 0.8076 (t0) REVERT: L 42 LEU cc_start: 0.9414 (mm) cc_final: 0.9211 (mm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1446 time to fit residues: 28.5241 Evaluate side-chains 132 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** B 181 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 = 0.3996 r_free = 0.3996 target = 0.132847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111413 restraints weight = 11821.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115424 restraints weight = 7538.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118332 restraints weight = 5208.091| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.189 Angle : 0.607 6.506 6055 Z= 0.305 Chirality : 0.042 0.130 688 Planarity : 0.005 0.043 748 Dihedral : 4.294 15.520 603 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.37), residues: 556 helix: 2.53 (0.34), residues: 224 sheet: 0.80 (0.52), residues: 88 loop : -1.38 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 33 HIS 0.001 0.001 HIS L 31 PHE 0.028 0.003 PHE B 62 TYR 0.027 0.002 TYR A 94 ARG 0.006 0.001 ARG H 98 *********************** 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 152 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8859 (m110) cc_final: 0.8572 (m110) REVERT: A 133 LEU cc_start: 0.8938 (pp) cc_final: 0.8570 (tt) REVERT: A 166 ASN cc_start: 0.8686 (t0) cc_final: 0.7931 (m110) REVERT: A 174 GLU cc_start: 0.9155 (mp0) cc_final: 0.8781 (mp0) REVERT: A 187 GLN cc_start: 0.8806 (mt0) cc_final: 0.8475 (mt0) REVERT: A 205 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 50 LYS cc_start: 0.9385 (tmtt) cc_final: 0.9103 (tmmt) REVERT: H 13 LYS cc_start: 0.7312 (tppt) cc_final: 0.6911 (mmmt) REVERT: H 46 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7432 (tm-30) REVERT: H 47 TRP cc_start: 0.8975 (t60) cc_final: 0.8477 (t60) REVERT: H 48 MET cc_start: 0.8266 (ppp) cc_final: 0.7646 (ppp) REVERT: H 57 ASP cc_start: 0.8862 (t0) cc_final: 0.8551 (t0) REVERT: H 81 MET cc_start: 0.4247 (tpt) cc_final: 0.3218 (tpt) REVERT: H 90 ASP cc_start: 0.8930 (m-30) cc_final: 0.8610 (m-30) REVERT: H 102 ASP cc_start: 0.8474 (t70) cc_final: 0.8092 (t0) REVERT: L 107 THR cc_start: 0.8431 (p) cc_final: 0.8198 (p) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1426 time to fit residues: 27.8995 Evaluate side-chains 130 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN ** B 181 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 = 0.3973 r_free = 0.3973 target = 0.130654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110685 restraints weight = 11841.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114329 restraints weight = 7594.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117064 restraints weight = 5289.644| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.206 Angle : 0.623 7.242 6055 Z= 0.316 Chirality : 0.042 0.138 688 Planarity : 0.004 0.046 748 Dihedral : 4.396 16.146 603 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.37), residues: 556 helix: 2.42 (0.35), residues: 224 sheet: 0.72 (0.51), residues: 88 loop : -1.36 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.002 0.001 HIS A 63 PHE 0.031 0.003 PHE A 62 TYR 0.029 0.002 TYR A 94 ARG 0.005 0.001 ARG H 50 *********************** 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 156 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8810 (m110) cc_final: 0.8497 (m110) REVERT: A 133 LEU cc_start: 0.8955 (pp) cc_final: 0.8703 (mm) REVERT: A 166 ASN cc_start: 0.8672 (t0) cc_final: 0.7982 (m-40) REVERT: A 171 ASN cc_start: 0.8984 (p0) cc_final: 0.8221 (p0) REVERT: A 174 GLU cc_start: 0.9166 (mp0) cc_final: 0.8815 (mp0) REVERT: A 187 GLN cc_start: 0.8786 (mt0) cc_final: 0.8505 (mt0) REVERT: A 205 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8618 (tm-30) REVERT: B 50 LYS cc_start: 0.9449 (tmtt) cc_final: 0.9164 (tmmt) REVERT: B 148 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8240 (pttt) REVERT: H 46 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7466 (tm-30) REVERT: H 47 TRP cc_start: 0.8957 (t60) cc_final: 0.8478 (t60) REVERT: H 48 MET cc_start: 0.8219 (ppp) cc_final: 0.7677 (ppp) REVERT: H 57 ASP cc_start: 0.8842 (t0) cc_final: 0.8557 (t0) REVERT: H 90 ASP cc_start: 0.8977 (m-30) cc_final: 0.8679 (m-30) REVERT: H 102 ASP cc_start: 0.8503 (t70) cc_final: 0.8104 (t70) REVERT: L 78 LEU cc_start: 0.7351 (tt) cc_final: 0.7080 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1336 time to fit residues: 27.1650 Evaluate side-chains 135 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.0040 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 140 ASN B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110727 restraints weight = 11529.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.114649 restraints weight = 7378.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117463 restraints weight = 5073.467| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4468 Z= 0.171 Angle : 0.616 7.641 6055 Z= 0.306 Chirality : 0.042 0.141 688 Planarity : 0.004 0.047 748 Dihedral : 4.266 15.315 603 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.37), residues: 556 helix: 2.49 (0.35), residues: 224 sheet: 0.69 (0.49), residues: 93 loop : -1.32 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 33 HIS 0.001 0.001 HIS B 63 PHE 0.026 0.002 PHE B 62 TYR 0.030 0.001 TYR A 94 ARG 0.004 0.001 ARG H 50 *********************** 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 165 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8966 (m110) cc_final: 0.8743 (m110) REVERT: A 133 LEU cc_start: 0.8992 (pp) cc_final: 0.8790 (mm) REVERT: A 166 ASN cc_start: 0.8720 (t0) cc_final: 0.8043 (m110) REVERT: A 171 ASN cc_start: 0.8833 (p0) cc_final: 0.8109 (p0) REVERT: A 174 GLU cc_start: 0.9188 (mp0) cc_final: 0.8872 (mp0) REVERT: A 187 GLN cc_start: 0.8785 (mt0) cc_final: 0.8496 (mt0) REVERT: A 205 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8641 (tm-30) REVERT: B 50 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9160 (tmmt) REVERT: B 148 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8162 (pttt) REVERT: H 13 LYS cc_start: 0.7225 (tppt) cc_final: 0.6847 (mmmt) REVERT: H 46 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7439 (tm-30) REVERT: H 47 TRP cc_start: 0.8941 (t60) cc_final: 0.8452 (t60) REVERT: H 48 MET cc_start: 0.8141 (ppp) cc_final: 0.7678 (ppp) REVERT: H 57 ASP cc_start: 0.8805 (t0) cc_final: 0.8504 (t0) REVERT: H 68 VAL cc_start: 0.8033 (t) cc_final: 0.6955 (t) REVERT: H 90 ASP cc_start: 0.9005 (m-30) cc_final: 0.8689 (m-30) REVERT: H 102 ASP cc_start: 0.8525 (t70) cc_final: 0.8059 (t70) REVERT: L 4 MET cc_start: 0.8698 (mpp) cc_final: 0.8475 (mpp) REVERT: L 78 LEU cc_start: 0.7332 (tt) cc_final: 0.7072 (tt) REVERT: L 102 THR cc_start: 0.8023 (m) cc_final: 0.7734 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1428 time to fit residues: 30.3976 Evaluate side-chains 143 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 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 = 0.3932 r_free = 0.3932 target = 0.127761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107288 restraints weight = 11558.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111056 restraints weight = 7397.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.113684 restraints weight = 5110.403| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4468 Z= 0.212 Angle : 0.680 12.806 6055 Z= 0.334 Chirality : 0.043 0.151 688 Planarity : 0.004 0.050 748 Dihedral : 4.444 16.552 603 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.38), residues: 556 helix: 2.37 (0.35), residues: 225 sheet: 0.51 (0.49), residues: 98 loop : -1.38 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.038 0.002 PHE A 62 TYR 0.027 0.002 TYR A 94 ARG 0.005 0.001 ARG H 50 *********************** 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 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 VAL cc_start: 0.9359 (t) cc_final: 0.9064 (t) REVERT: A 59 ASN cc_start: 0.9043 (m110) cc_final: 0.8150 (m110) REVERT: A 166 ASN cc_start: 0.8724 (t0) cc_final: 0.8080 (m110) REVERT: A 171 ASN cc_start: 0.8877 (p0) cc_final: 0.8086 (p0) REVERT: A 174 GLU cc_start: 0.9198 (mp0) cc_final: 0.8874 (mp0) REVERT: A 187 GLN cc_start: 0.8782 (mt0) cc_final: 0.8485 (mt0) REVERT: A 205 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8686 (tm-30) REVERT: B 50 LYS cc_start: 0.9459 (tmtt) cc_final: 0.9130 (tmmt) REVERT: B 148 LYS cc_start: 0.8690 (mmtm) cc_final: 0.8308 (pttt) REVERT: H 46 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 47 TRP cc_start: 0.8991 (t60) cc_final: 0.8566 (t60) REVERT: H 48 MET cc_start: 0.8277 (ppp) cc_final: 0.7707 (ppp) REVERT: H 57 ASP cc_start: 0.8847 (t0) cc_final: 0.8520 (t0) REVERT: H 102 ASP cc_start: 0.8513 (t70) cc_final: 0.8068 (t70) REVERT: L 4 MET cc_start: 0.8640 (mpp) cc_final: 0.8409 (mpp) REVERT: L 78 LEU cc_start: 0.7449 (tt) cc_final: 0.7216 (tt) REVERT: L 102 THR cc_start: 0.8096 (m) cc_final: 0.7773 (m) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1368 time to fit residues: 28.0509 Evaluate side-chains 135 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 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 = 0.3956 r_free = 0.3956 target = 0.129300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108880 restraints weight = 11716.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112648 restraints weight = 7422.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115341 restraints weight = 5123.025| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.184 Angle : 0.663 8.973 6055 Z= 0.325 Chirality : 0.044 0.171 688 Planarity : 0.005 0.050 748 Dihedral : 4.408 15.462 603 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.38), residues: 556 helix: 2.30 (0.35), residues: 224 sheet: 0.57 (0.48), residues: 103 loop : -1.35 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.017 0.002 HIS B 145 PHE 0.026 0.002 PHE A 62 TYR 0.030 0.002 TYR A 94 ARG 0.005 0.001 ARG H 50 *********************** 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 160 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8710 (m110) cc_final: 0.8338 (m-40) REVERT: A 166 ASN cc_start: 0.8707 (t0) cc_final: 0.8134 (m-40) REVERT: A 171 ASN cc_start: 0.8873 (p0) cc_final: 0.8121 (p0) REVERT: A 174 GLU cc_start: 0.9216 (mp0) cc_final: 0.8920 (mp0) REVERT: A 187 GLN cc_start: 0.8807 (mt0) cc_final: 0.8497 (mt0) REVERT: A 202 PHE cc_start: 0.8034 (t80) cc_final: 0.7805 (t80) REVERT: A 205 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 50 LYS cc_start: 0.9469 (tmtt) cc_final: 0.9144 (tmmt) REVERT: B 59 ASN cc_start: 0.8697 (m110) cc_final: 0.8276 (m110) REVERT: B 148 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8229 (pttt) REVERT: H 18 VAL cc_start: 0.8274 (p) cc_final: 0.7740 (p) REVERT: H 46 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7548 (tm-30) REVERT: H 47 TRP cc_start: 0.8971 (t60) cc_final: 0.8566 (t60) REVERT: H 48 MET cc_start: 0.8148 (ppp) cc_final: 0.7500 (ppp) REVERT: H 57 ASP cc_start: 0.8798 (t0) cc_final: 0.8501 (t0) REVERT: H 102 ASP cc_start: 0.8517 (t70) cc_final: 0.8023 (t70) REVERT: L 78 LEU cc_start: 0.7378 (tt) cc_final: 0.7124 (tt) REVERT: L 102 THR cc_start: 0.8054 (m) cc_final: 0.7717 (m) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1410 time to fit residues: 29.0962 Evaluate side-chains 141 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 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 = 0.3957 r_free = 0.3957 target = 0.129604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109011 restraints weight = 11233.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112831 restraints weight = 7093.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.115605 restraints weight = 4856.212| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4468 Z= 0.180 Angle : 0.655 9.260 6055 Z= 0.324 Chirality : 0.043 0.164 688 Planarity : 0.004 0.050 748 Dihedral : 4.391 15.968 603 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.37), residues: 556 helix: 2.25 (0.34), residues: 224 sheet: 0.48 (0.48), residues: 103 loop : -1.37 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 33 HIS 0.013 0.002 HIS B 145 PHE 0.026 0.002 PHE A 62 TYR 0.030 0.002 TYR A 94 ARG 0.004 0.000 ARG H 50 ********************** 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 161 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7466 (t0) cc_final: 0.7244 (t0) REVERT: A 166 ASN cc_start: 0.8800 (t0) cc_final: 0.8039 (m-40) REVERT: A 171 ASN cc_start: 0.8796 (p0) cc_final: 0.8027 (p0) REVERT: A 174 GLU cc_start: 0.9220 (mp0) cc_final: 0.8923 (mp0) REVERT: A 187 GLN cc_start: 0.8782 (mt0) cc_final: 0.8460 (mt0) REVERT: A 205 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8645 (tm-30) REVERT: B 50 LYS cc_start: 0.9499 (tmtt) cc_final: 0.9164 (tmmt) REVERT: B 148 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8260 (pttt) REVERT: H 18 VAL cc_start: 0.8520 (p) cc_final: 0.7973 (p) REVERT: H 46 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7814 (tm-30) REVERT: H 47 TRP cc_start: 0.8955 (t60) cc_final: 0.8420 (t60) REVERT: H 48 MET cc_start: 0.8165 (ppp) cc_final: 0.7464 (ppp) REVERT: H 57 ASP cc_start: 0.8860 (t0) cc_final: 0.8511 (t0) REVERT: H 102 ASP cc_start: 0.8537 (t70) cc_final: 0.8051 (t70) REVERT: L 78 LEU cc_start: 0.7428 (tt) cc_final: 0.7185 (tt) REVERT: L 102 THR cc_start: 0.7997 (m) cc_final: 0.7529 (m) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1375 time to fit residues: 28.5996 Evaluate side-chains 141 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 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 = 0.3966 r_free = 0.3966 target = 0.130158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109256 restraints weight = 11959.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113031 restraints weight = 7557.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.115758 restraints weight = 5219.951| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4468 Z= 0.173 Angle : 0.656 9.296 6055 Z= 0.322 Chirality : 0.043 0.163 688 Planarity : 0.005 0.058 748 Dihedral : 4.313 15.996 603 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.38), residues: 556 helix: 2.16 (0.34), residues: 224 sheet: 0.50 (0.49), residues: 103 loop : -1.27 (0.45), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 105 HIS 0.011 0.001 HIS B 145 PHE 0.043 0.002 PHE B 62 TYR 0.030 0.002 TYR A 94 ARG 0.002 0.000 ARG H 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.62 seconds wall clock time: 31 minutes 11.25 seconds (1871.25 seconds total)