Starting phenix.real_space_refine on Thu Mar 6 01:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y97_10733/03_2025/6y97_10733.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y97_10733/03_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_10733/03_2025/6y97_10733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2025/6y97_10733.map" model { file = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_2025/6y97_10733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y97_10733/03_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-5624/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: 3.52, per 1000 atoms: 0.81 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: 1.06 Conformation dependent library (CDL) restraints added in 525.2 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: 0.44 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: 0.99 Time building geometry restraints manager: 1.26 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: 2.980 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.690 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- 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 : 0.377 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: 0.1326 time to fit residues: 27.8341 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 : 0.443 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.138074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117275 restraints weight = 11544.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.120933 restraints weight = 7626.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123641 restraints weight = 5375.894| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8745 (pp) cc_final: 0.8333 (tt) REVERT: A 166 ASN cc_start: 0.8713 (t0) cc_final: 0.8468 (t0) REVERT: A 187 GLN cc_start: 0.8762 (mt0) cc_final: 0.8447 (mt0) REVERT: B 50 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9068 (tmmt) REVERT: B 124 LEU cc_start: 0.9507 (mm) cc_final: 0.9252 (mt) REVERT: H 27 TYR cc_start: 0.8595 (p90) cc_final: 0.8228 (p90) REVERT: H 46 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 47 TRP cc_start: 0.9099 (t60) cc_final: 0.8422 (t60) REVERT: H 48 MET cc_start: 0.8336 (ppp) cc_final: 0.7727 (ppp) REVERT: H 57 ASP cc_start: 0.8944 (t0) cc_final: 0.8687 (t0) REVERT: H 81 MET cc_start: 0.3692 (tpt) cc_final: 0.2985 (tpt) REVERT: H 90 ASP cc_start: 0.8788 (m-30) cc_final: 0.8440 (m-30) REVERT: L 42 LEU cc_start: 0.9004 (mm) cc_final: 0.8781 (mm) REVERT: L 107 THR cc_start: 0.8109 (p) cc_final: 0.7884 (p) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1282 time to fit residues: 26.0965 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 : 0.776 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115490 restraints weight = 11503.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.119277 restraints weight = 7484.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122129 restraints weight = 5238.808| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3980 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= 0.188 Angle : 0.603 6.521 6055 Z= 0.307 Chirality : 0.042 0.132 688 Planarity : 0.005 0.051 748 Dihedral : 4.130 17.827 603 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.21 % Allowed : 4.37 % Favored : 95.43 % 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: 1.08 (0.38), residues: 556 helix: 2.60 (0.35), residues: 225 sheet: 0.92 (0.55), residues: 82 loop : -1.23 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 89 HIS 0.001 0.001 HIS B 63 PHE 0.020 0.002 PHE A 62 TYR 0.036 0.002 TYR A 94 ARG 0.002 0.000 ARG L 82 *********************** 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 156 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8820 (pp) cc_final: 0.8408 (tt) REVERT: A 166 ASN cc_start: 0.8591 (t0) cc_final: 0.8298 (t0) REVERT: A 187 GLN cc_start: 0.8843 (mt0) cc_final: 0.8573 (mt0) REVERT: B 50 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9105 (tmmt) REVERT: B 71 MET cc_start: 0.5764 (ptp) cc_final: 0.5457 (ptp) REVERT: H 13 LYS cc_start: 0.7324 (tppt) cc_final: 0.7007 (mmmt) REVERT: H 46 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7677 (tm-30) REVERT: H 47 TRP cc_start: 0.9060 (t60) cc_final: 0.8420 (t60) REVERT: H 48 MET cc_start: 0.8184 (ppp) cc_final: 0.7591 (ppp) REVERT: H 57 ASP cc_start: 0.8894 (t0) cc_final: 0.8555 (t0) REVERT: H 90 ASP cc_start: 0.8862 (m-30) cc_final: 0.8543 (m-30) REVERT: L 42 LEU cc_start: 0.9400 (mm) cc_final: 0.9081 (mm) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.1368 time to fit residues: 27.6059 Evaluate side-chains 133 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.1980 chunk 26 optimal weight: 0.0050 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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** H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114729 restraints weight = 11504.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.118652 restraints weight = 7511.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.121573 restraints weight = 5235.749| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4310 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= 0.172 Angle : 0.579 6.541 6055 Z= 0.293 Chirality : 0.041 0.133 688 Planarity : 0.005 0.045 748 Dihedral : 4.138 15.879 603 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % 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 (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: 1.10 (0.38), residues: 556 helix: 2.68 (0.35), residues: 225 sheet: 1.00 (0.55), residues: 82 loop : -1.31 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 33 HIS 0.001 0.000 HIS L 31 PHE 0.018 0.002 PHE A 200 TYR 0.025 0.002 TYR A 94 ARG 0.004 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 157 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8710 (m110) cc_final: 0.8407 (m110) REVERT: A 133 LEU cc_start: 0.8902 (pp) cc_final: 0.8480 (tt) REVERT: A 166 ASN cc_start: 0.8765 (t0) cc_final: 0.7910 (m-40) REVERT: A 174 GLU cc_start: 0.9077 (mp0) cc_final: 0.8767 (mp0) REVERT: A 183 CYS cc_start: 0.7619 (p) cc_final: 0.7401 (p) REVERT: A 187 GLN cc_start: 0.8814 (mt0) cc_final: 0.8554 (mt0) REVERT: B 50 LYS cc_start: 0.9385 (tmtt) cc_final: 0.9103 (tmmt) REVERT: B 59 ASN cc_start: 0.8310 (m110) cc_final: 0.7825 (m110) REVERT: B 71 MET cc_start: 0.5796 (ptp) cc_final: 0.5489 (ptp) REVERT: H 13 LYS cc_start: 0.7181 (tppt) cc_final: 0.6854 (mmmt) REVERT: H 19 LYS cc_start: 0.8372 (mmtm) cc_final: 0.7965 (tppp) REVERT: H 47 TRP cc_start: 0.8984 (t60) cc_final: 0.8405 (t60) REVERT: H 48 MET cc_start: 0.8137 (ppp) cc_final: 0.7471 (ppp) REVERT: H 57 ASP cc_start: 0.8918 (t0) cc_final: 0.8639 (t0) REVERT: H 90 ASP cc_start: 0.8863 (m-30) cc_final: 0.8550 (m-30) REVERT: H 102 ASP cc_start: 0.8325 (t70) cc_final: 0.8020 (t0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1293 time to fit residues: 26.3806 Evaluate side-chains 136 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.131929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110810 restraints weight = 11886.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114704 restraints weight = 7614.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.117555 restraints weight = 5267.588| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4857 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 : 0.614 6.327 6055 Z= 0.310 Chirality : 0.042 0.133 688 Planarity : 0.004 0.046 748 Dihedral : 4.310 16.562 603 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % 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 (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: 0.91 (0.37), residues: 556 helix: 2.51 (0.34), residues: 224 sheet: 0.80 (0.53), residues: 88 loop : -1.40 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.027 0.003 PHE A 62 TYR 0.026 0.002 TYR A 94 ARG 0.006 0.001 ARG H 50 *********************** 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 156 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8939 (m110) cc_final: 0.8643 (m110) REVERT: A 133 LEU cc_start: 0.8942 (pp) cc_final: 0.8548 (tt) REVERT: A 166 ASN cc_start: 0.8670 (t0) cc_final: 0.7909 (m110) REVERT: A 174 GLU cc_start: 0.9142 (mp0) cc_final: 0.8750 (mp0) REVERT: A 187 GLN cc_start: 0.8750 (mt0) cc_final: 0.8385 (mt0) REVERT: B 50 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9120 (tmmt) REVERT: B 59 ASN cc_start: 0.8273 (m110) cc_final: 0.7812 (m110) REVERT: B 165 TYR cc_start: 0.8159 (m-80) cc_final: 0.7941 (m-10) REVERT: H 13 LYS cc_start: 0.7314 (tppt) cc_final: 0.6977 (mmmt) REVERT: H 46 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 47 TRP cc_start: 0.9007 (t60) cc_final: 0.8522 (t60) REVERT: H 48 MET cc_start: 0.8294 (ppp) cc_final: 0.7508 (ppp) REVERT: H 57 ASP cc_start: 0.8882 (t0) cc_final: 0.8573 (t0) REVERT: H 70 ILE cc_start: 0.8358 (pt) cc_final: 0.8146 (pt) REVERT: H 81 MET cc_start: 0.4626 (tpt) cc_final: 0.3541 (tpt) REVERT: H 90 ASP cc_start: 0.8946 (m-30) cc_final: 0.8629 (m-30) REVERT: H 102 ASP cc_start: 0.8457 (t70) cc_final: 0.8091 (t0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1347 time to fit residues: 27.1555 Evaluate side-chains 133 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.6980 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** 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 = 0.3888 r_free = 0.3888 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105352 restraints weight = 11756.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109023 restraints weight = 7449.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111672 restraints weight = 5114.103| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5708 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= 0.249 Angle : 0.664 8.065 6055 Z= 0.341 Chirality : 0.043 0.142 688 Planarity : 0.005 0.046 748 Dihedral : 4.735 19.560 603 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: 0.64 (0.37), residues: 556 helix: 2.30 (0.35), residues: 223 sheet: 0.48 (0.50), residues: 88 loop : -1.46 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.034 0.003 PHE B 62 TYR 0.029 0.002 TYR A 94 ARG 0.007 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 159 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9105 (m110) cc_final: 0.8868 (m110) REVERT: A 166 ASN cc_start: 0.8761 (t0) cc_final: 0.8051 (m110) REVERT: A 174 GLU cc_start: 0.9223 (mp0) cc_final: 0.8678 (mp0) REVERT: A 187 GLN cc_start: 0.8807 (mt0) cc_final: 0.8490 (mt0) REVERT: B 50 LYS cc_start: 0.9475 (tmtt) cc_final: 0.9163 (tmmt) REVERT: B 59 ASN cc_start: 0.8452 (m110) cc_final: 0.7973 (m110) REVERT: B 148 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8180 (pttt) REVERT: B 165 TYR cc_start: 0.8059 (m-80) cc_final: 0.7858 (m-10) REVERT: H 46 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 47 TRP cc_start: 0.8992 (t60) cc_final: 0.8567 (t60) REVERT: H 48 MET cc_start: 0.8322 (ppp) cc_final: 0.7651 (ppp) REVERT: H 57 ASP cc_start: 0.8879 (t0) cc_final: 0.8544 (t0) REVERT: H 68 VAL cc_start: 0.8208 (t) cc_final: 0.7430 (t) REVERT: H 81 MET cc_start: 0.4804 (tpt) cc_final: 0.4123 (tmm) REVERT: H 90 ASP cc_start: 0.9077 (m-30) cc_final: 0.8748 (m-30) REVERT: H 102 ASP cc_start: 0.8518 (t70) cc_final: 0.8089 (t70) REVERT: L 78 LEU cc_start: 0.7480 (tt) cc_final: 0.7273 (tt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1344 time to fit residues: 27.9035 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 : 0.475 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107415 restraints weight = 11938.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.111101 restraints weight = 7613.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113794 restraints weight = 5267.412| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5885 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= 0.205 Angle : 0.654 7.371 6055 Z= 0.330 Chirality : 0.043 0.142 688 Planarity : 0.005 0.048 748 Dihedral : 4.578 17.526 603 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 0.67 (0.37), residues: 556 helix: 2.36 (0.35), residues: 223 sheet: 0.41 (0.51), residues: 88 loop : -1.46 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 33 HIS 0.002 0.001 HIS B 145 PHE 0.028 0.002 PHE B 62 TYR 0.031 0.002 TYR A 94 ARG 0.005 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 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9131 (m110) cc_final: 0.8857 (m110) REVERT: A 166 ASN cc_start: 0.8786 (t0) cc_final: 0.8176 (m110) REVERT: A 171 ASN cc_start: 0.8900 (p0) cc_final: 0.8120 (p0) REVERT: A 174 GLU cc_start: 0.9221 (mp0) cc_final: 0.8826 (mp0) REVERT: A 187 GLN cc_start: 0.8823 (mt0) cc_final: 0.8477 (mt0) REVERT: B 50 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9138 (tmmt) REVERT: B 59 ASN cc_start: 0.8678 (m110) cc_final: 0.8346 (m110) REVERT: B 165 TYR cc_start: 0.8115 (m-80) cc_final: 0.7842 (m-80) REVERT: H 46 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7477 (tm-30) REVERT: H 47 TRP cc_start: 0.9007 (t60) cc_final: 0.8553 (t60) REVERT: H 48 MET cc_start: 0.8281 (ppp) cc_final: 0.7737 (ppp) REVERT: H 57 ASP cc_start: 0.8867 (t0) cc_final: 0.8515 (t0) REVERT: H 68 VAL cc_start: 0.7867 (t) cc_final: 0.6955 (t) REVERT: H 102 ASP cc_start: 0.8591 (t70) cc_final: 0.8093 (t70) REVERT: H 106 LEU cc_start: 0.9296 (tt) cc_final: 0.9092 (tt) REVERT: L 4 MET cc_start: 0.8699 (mpp) cc_final: 0.8419 (mpp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1289 time to fit residues: 26.6558 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 : 0.448 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** B 140 ASN B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105113 restraints weight = 11691.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108650 restraints weight = 7504.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111256 restraints weight = 5189.908| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4468 Z= 0.236 Angle : 0.686 6.541 6055 Z= 0.351 Chirality : 0.044 0.153 688 Planarity : 0.005 0.051 748 Dihedral : 4.807 19.875 603 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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: 0.45 (0.37), residues: 556 helix: 2.18 (0.35), residues: 223 sheet: 0.28 (0.50), residues: 88 loop : -1.56 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 109 HIS 0.003 0.001 HIS A 145 PHE 0.022 0.003 PHE B 62 TYR 0.029 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 160 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 VAL cc_start: 0.9423 (t) cc_final: 0.8927 (t) REVERT: A 59 ASN cc_start: 0.9209 (m110) cc_final: 0.8142 (m110) REVERT: A 171 ASN cc_start: 0.8865 (p0) cc_final: 0.8061 (p0) REVERT: A 174 GLU cc_start: 0.9300 (mp0) cc_final: 0.8904 (mp0) REVERT: A 187 GLN cc_start: 0.8839 (mt0) cc_final: 0.8508 (mt0) REVERT: B 50 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9149 (tmmt) REVERT: B 165 TYR cc_start: 0.8038 (m-80) cc_final: 0.7796 (m-80) REVERT: H 46 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7475 (tm-30) REVERT: H 47 TRP cc_start: 0.9041 (t60) cc_final: 0.8505 (t60) REVERT: H 48 MET cc_start: 0.8422 (ppp) cc_final: 0.7944 (ppp) REVERT: H 57 ASP cc_start: 0.8852 (t0) cc_final: 0.8467 (t0) REVERT: H 102 ASP cc_start: 0.8535 (t70) cc_final: 0.8020 (t70) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1292 time to fit residues: 27.0024 Evaluate side-chains 140 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** B 140 ASN B 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.125677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106289 restraints weight = 11862.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109912 restraints weight = 7460.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112537 restraints weight = 5099.491| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4468 Z= 0.214 Angle : 0.673 8.517 6055 Z= 0.340 Chirality : 0.044 0.157 688 Planarity : 0.005 0.052 748 Dihedral : 4.731 18.659 603 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % 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: 0.51 (0.37), residues: 556 helix: 2.15 (0.35), residues: 223 sheet: 0.50 (0.52), residues: 85 loop : -1.51 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.038 0.003 PHE B 62 TYR 0.031 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 163 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8899 (m110) cc_final: 0.8507 (m-40) REVERT: A 166 ASN cc_start: 0.8851 (t0) cc_final: 0.8244 (m-40) REVERT: A 171 ASN cc_start: 0.8829 (p0) cc_final: 0.8074 (p0) REVERT: A 174 GLU cc_start: 0.9340 (mp0) cc_final: 0.8887 (mp0) REVERT: A 187 GLN cc_start: 0.8817 (mt0) cc_final: 0.8511 (mt0) REVERT: A 202 PHE cc_start: 0.8045 (t80) cc_final: 0.7812 (t80) REVERT: B 50 LYS cc_start: 0.9490 (tmtt) cc_final: 0.9189 (tmmt) REVERT: B 58 MET cc_start: 0.8821 (ttp) cc_final: 0.8583 (tmm) REVERT: B 59 ASN cc_start: 0.8903 (m110) cc_final: 0.8565 (m110) REVERT: H 46 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7533 (tm-30) REVERT: H 47 TRP cc_start: 0.8983 (t60) cc_final: 0.8467 (t60) REVERT: H 48 MET cc_start: 0.8261 (ppp) cc_final: 0.7803 (ppp) REVERT: H 57 ASP cc_start: 0.8798 (t0) cc_final: 0.8490 (t0) REVERT: H 68 VAL cc_start: 0.8225 (t) cc_final: 0.7598 (t) REVERT: H 102 ASP cc_start: 0.8550 (t70) cc_final: 0.8041 (t70) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1415 time to fit residues: 30.4538 Evaluate side-chains 140 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 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 = 0.3901 r_free = 0.3901 target = 0.125295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.105747 restraints weight = 11533.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109384 restraints weight = 7233.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.112023 restraints weight = 4948.970| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4468 Z= 0.208 Angle : 0.680 9.631 6055 Z= 0.341 Chirality : 0.044 0.166 688 Planarity : 0.005 0.057 748 Dihedral : 4.690 16.773 603 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.20 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: 0.59 (0.37), residues: 556 helix: 2.21 (0.35), residues: 217 sheet: 0.46 (0.51), residues: 95 loop : -1.40 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 105 HIS 0.006 0.001 HIS B 145 PHE 0.038 0.002 PHE B 62 TYR 0.031 0.002 TYR A 94 ARG 0.004 0.001 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 162 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8880 (m110) cc_final: 0.8447 (m110) REVERT: A 166 ASN cc_start: 0.8841 (t0) cc_final: 0.8220 (m110) REVERT: A 171 ASN cc_start: 0.8794 (p0) cc_final: 0.8051 (p0) REVERT: A 174 GLU cc_start: 0.9351 (mp0) cc_final: 0.8899 (mp0) REVERT: A 187 GLN cc_start: 0.8801 (mt0) cc_final: 0.8482 (mt0) REVERT: B 50 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9181 (tmmt) REVERT: B 58 MET cc_start: 0.8900 (ttp) cc_final: 0.8097 (tmm) REVERT: B 59 ASN cc_start: 0.9021 (m110) cc_final: 0.8601 (m110) REVERT: H 18 VAL cc_start: 0.8445 (p) cc_final: 0.8224 (p) REVERT: H 46 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7462 (tm-30) REVERT: H 47 TRP cc_start: 0.8946 (t60) cc_final: 0.8465 (t60) REVERT: H 48 MET cc_start: 0.8319 (ppp) cc_final: 0.7846 (ppp) REVERT: H 57 ASP cc_start: 0.8824 (t0) cc_final: 0.8475 (t0) REVERT: H 68 VAL cc_start: 0.8241 (t) cc_final: 0.7215 (t) REVERT: H 102 ASP cc_start: 0.8621 (t70) cc_final: 0.8097 (t70) REVERT: L 102 THR cc_start: 0.8079 (m) cc_final: 0.7814 (m) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1331 time to fit residues: 28.0518 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 : 0.453 ------------------------------------------------------------------------------- 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: 0.0980 chunk 32 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3934 r_free = 0.3934 target = 0.127438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107562 restraints weight = 11988.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111330 restraints weight = 7486.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.114059 restraints weight = 5096.284| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4468 Z= 0.187 Angle : 0.667 9.596 6055 Z= 0.333 Chirality : 0.044 0.165 688 Planarity : 0.005 0.050 748 Dihedral : 4.546 15.836 603 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: 0.65 (0.37), residues: 556 helix: 2.29 (0.35), residues: 217 sheet: 0.29 (0.51), residues: 98 loop : -1.32 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 105 HIS 0.009 0.001 HIS B 145 PHE 0.015 0.002 PHE B 146 TYR 0.031 0.002 TYR A 94 ARG 0.005 0.001 ARG H 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.46 seconds wall clock time: 29 minutes 58.85 seconds (1798.85 seconds total)