Starting phenix.real_space_refine on Thu Mar 6 04:22:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171.map" model { file = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p2p_13171/03_2025/7p2p_13171_neut.cif" } resolution = 4.9 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= 0.002 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 23 5.16 5 C 3109 2.51 5 N 785 2.21 5 O 866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 4783 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1189 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.55, per 1000 atoms: 0.74 Number of scatterers: 4783 At special positions: 0 Unit cell: (79.38, 84.24, 131.22, 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 23 16.00 O 866 8.00 N 785 7.00 C 3109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 606.4 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 15.0% 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 15 through 43 Processing helix chain 'A' and resid 148 through 158 removed outlier: 4.210A pdb=" N VAL A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 30 Processing helix chain 'C' and resid 53 through 72 Processing helix chain 'C' and resid 79 through 104 Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.894A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 removed outlier: 3.559A pdb=" N ALA C 207 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 208 through 224 removed outlier: 4.018A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 110 Processing helix chain 'D' and resid 111 through 131 removed outlier: 4.352A pdb=" N THR D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 141 through 144 removed outlier: 4.021A pdb=" N TRP D 144 " --> pdb=" O PRO D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.151A pdb=" N ILE A 101 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 102 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.535A pdb=" N PHE A 111 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.078A pdb=" N LEU B 48 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR B 67 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN B 50 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 65 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 64 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 90 removed outlier: 4.321A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 151 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 88 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 147 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 146 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B 164 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TRP B 148 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 162 " --> pdb=" O TRP B 148 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 150 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL B 160 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77 removed outlier: 4.313A pdb=" N VAL C 142 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 621 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: 1.22 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 816 1.33 - 1.45: 1298 1.45 - 1.57: 2744 1.57 - 1.69: 1 1.69 - 1.81: 41 Bond restraints: 4900 Sorted by residual: bond pdb=" N LEU D 131 " pdb=" CA LEU D 131 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.86e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" N LEU A 69 " pdb=" CA LEU A 69 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N ILE D 136 " pdb=" CA ILE D 136 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" C PRO D 135 " pdb=" O PRO D 135 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.26e-02 6.30e+03 6.63e+00 ... (remaining 4895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 6279 2.07 - 4.14: 270 4.14 - 6.21: 48 6.21 - 8.28: 24 8.28 - 10.35: 13 Bond angle restraints: 6634 Sorted by residual: angle pdb=" N PRO D 141 " pdb=" CA PRO D 141 " pdb=" C PRO D 141 " ideal model delta sigma weight residual 113.57 106.87 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C LYS B 49 " pdb=" N ASN B 50 " pdb=" CA ASN B 50 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C CYS B 26 " pdb=" N PHE B 27 " pdb=" CA PHE B 27 " ideal model delta sigma weight residual 121.66 113.71 7.95 1.76e+00 3.23e-01 2.04e+01 ... (remaining 6629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 2808 21.45 - 42.90: 140 42.90 - 64.35: 8 64.35 - 85.80: 8 85.80 - 107.25: 4 Dihedral angle restraints: 2968 sinusoidal: 1262 harmonic: 1706 Sorted by residual: dihedral pdb=" CA LYS C 111 " pdb=" C LYS C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU D 75 " pdb=" C LEU D 75 " pdb=" N PRO D 76 " pdb=" CA PRO D 76 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO D 133 " pdb=" C PRO D 133 " pdb=" N TRP D 134 " pdb=" CA TRP D 134 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 707 0.122 - 0.244: 47 0.244 - 0.366: 2 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 757 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE A 68 " pdb=" N PHE A 68 " pdb=" C PHE A 68 " pdb=" CB PHE A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 754 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 22 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL A 22 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 22 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 23 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 216 " 0.013 2.00e-02 2.50e+03 1.71e-02 4.37e+00 pdb=" CG HIS C 216 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS C 216 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS C 216 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS C 216 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 216 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 24 " 0.012 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE B 24 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 24 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 24 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 24 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 24 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 24 " -0.000 2.00e-02 2.50e+03 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1464 2.84 - 3.35: 4304 3.35 - 3.87: 7635 3.87 - 4.38: 7919 4.38 - 4.90: 13585 Nonbonded interactions: 34907 Sorted by model distance: nonbonded pdb=" O THR A 43 " pdb=" ND2 ASN A 71 " model vdw 2.325 3.120 nonbonded pdb=" O ILE A 87 " pdb=" N GLU A 91 " model vdw 2.343 3.120 nonbonded pdb=" O SER D 126 " pdb=" OG1 THR D 130 " model vdw 2.349 3.040 nonbonded pdb=" O TRP C 51 " pdb=" OG1 THR D 77 " model vdw 2.351 3.040 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.353 3.040 ... (remaining 34902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.850 Find NCS groups from input model: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.005 0.054 4900 Z= 0.315 Angle : 1.104 10.353 6634 Z= 0.564 Chirality : 0.067 0.610 757 Planarity : 0.007 0.046 820 Dihedral : 13.150 107.252 1868 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.19 % Allowed : 8.06 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.94 (0.28), residues: 579 helix: -1.72 (0.27), residues: 208 sheet: -1.10 (0.63), residues: 57 loop : -3.72 (0.28), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 80 HIS 0.021 0.002 HIS C 216 PHE 0.036 0.004 PHE B 24 TYR 0.018 0.002 TYR B 174 ARG 0.005 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8498 (m-80) cc_final: 0.8258 (m-80) REVERT: A 24 ASN cc_start: 0.8489 (p0) cc_final: 0.8284 (p0) REVERT: A 29 VAL cc_start: 0.9273 (m) cc_final: 0.8913 (p) REVERT: A 40 MET cc_start: 0.7844 (mmm) cc_final: 0.7534 (mmm) REVERT: A 67 LEU cc_start: 0.8969 (mm) cc_final: 0.8698 (mm) REVERT: A 126 TYR cc_start: 0.6041 (m-80) cc_final: 0.4927 (m-80) REVERT: A 135 LYS cc_start: 0.8748 (pttt) cc_final: 0.8203 (tptt) REVERT: A 137 ASP cc_start: 0.7849 (m-30) cc_final: 0.7579 (p0) REVERT: A 143 ARG cc_start: 0.7333 (mmm160) cc_final: 0.6117 (ptt180) REVERT: A 156 MET cc_start: 0.8235 (tpt) cc_final: 0.7822 (tpt) REVERT: B 70 ILE cc_start: 0.8739 (pp) cc_final: 0.8453 (mm) REVERT: B 174 TYR cc_start: 0.7391 (t80) cc_final: 0.6564 (t80) REVERT: C 69 LEU cc_start: 0.8353 (tm) cc_final: 0.7845 (pp) REVERT: C 129 THR cc_start: 0.8495 (m) cc_final: 0.8290 (p) REVERT: D 90 MET cc_start: 0.4131 (mmt) cc_final: 0.3533 (tpt) REVERT: D 116 VAL cc_start: 0.7631 (t) cc_final: 0.7388 (t) REVERT: D 149 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8261 (mm-30) REVERT: D 150 SER cc_start: 0.8327 (m) cc_final: 0.7955 (t) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.2394 time to fit residues: 55.3384 Evaluate side-chains 109 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 108 HIS A 128 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.109158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.099279 restraints weight = 34865.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100799 restraints weight = 23616.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.101896 restraints weight = 17168.309| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4900 Z= 0.175 Angle : 0.741 8.233 6634 Z= 0.371 Chirality : 0.051 0.438 757 Planarity : 0.005 0.052 820 Dihedral : 9.910 72.414 732 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 5.76 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.67 (0.32), residues: 579 helix: -0.01 (0.34), residues: 211 sheet: -1.14 (0.63), residues: 65 loop : -3.40 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.016 0.001 HIS C 216 PHE 0.028 0.002 PHE C 94 TYR 0.022 0.002 TYR D 117 ARG 0.006 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8411 (m-80) cc_final: 0.7910 (m-80) REVERT: A 24 ASN cc_start: 0.8775 (p0) cc_final: 0.8503 (p0) REVERT: A 75 ASP cc_start: 0.5221 (p0) cc_final: 0.4967 (p0) REVERT: A 135 LYS cc_start: 0.8900 (pttt) cc_final: 0.8155 (tptp) REVERT: A 143 ARG cc_start: 0.7352 (mmm160) cc_final: 0.6014 (ptt180) REVERT: A 156 MET cc_start: 0.8050 (tpt) cc_final: 0.7723 (tpt) REVERT: B 69 ASP cc_start: 0.7556 (m-30) cc_final: 0.7234 (m-30) REVERT: B 70 ILE cc_start: 0.8825 (pt) cc_final: 0.8112 (mp) REVERT: C 84 ARG cc_start: 0.8643 (mmp80) cc_final: 0.8066 (mmp80) REVERT: C 129 THR cc_start: 0.8465 (m) cc_final: 0.8256 (p) REVERT: D 86 LEU cc_start: 0.8021 (mm) cc_final: 0.7737 (tp) REVERT: D 90 MET cc_start: 0.4559 (mmt) cc_final: 0.3880 (tpt) REVERT: D 103 PHE cc_start: 0.8745 (p90) cc_final: 0.8532 (p90) REVERT: D 116 VAL cc_start: 0.8408 (t) cc_final: 0.7763 (t) REVERT: D 150 SER cc_start: 0.8276 (m) cc_final: 0.7883 (t) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.2111 time to fit residues: 38.0528 Evaluate side-chains 111 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 118 ASN A 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.106613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.096833 restraints weight = 34594.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.098229 restraints weight = 23805.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.099269 restraints weight = 17435.437| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4900 Z= 0.171 Angle : 0.728 8.816 6634 Z= 0.361 Chirality : 0.050 0.387 757 Planarity : 0.006 0.093 820 Dihedral : 9.188 64.384 732 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.33), residues: 579 helix: 0.54 (0.36), residues: 212 sheet: -0.86 (0.61), residues: 68 loop : -3.22 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.016 0.001 HIS C 216 PHE 0.031 0.002 PHE B 12 TYR 0.026 0.002 TYR D 117 ARG 0.009 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8574 (t80) cc_final: 0.8265 (t80) REVERT: A 67 LEU cc_start: 0.8594 (mm) cc_final: 0.8363 (mm) REVERT: A 75 ASP cc_start: 0.5589 (p0) cc_final: 0.5387 (p0) REVERT: A 135 LYS cc_start: 0.8910 (pttt) cc_final: 0.8114 (tptp) REVERT: A 143 ARG cc_start: 0.7452 (mmm160) cc_final: 0.6119 (ptt180) REVERT: A 156 MET cc_start: 0.7994 (tpt) cc_final: 0.7681 (tpt) REVERT: B 69 ASP cc_start: 0.7957 (m-30) cc_final: 0.7532 (m-30) REVERT: B 96 LYS cc_start: 0.8682 (tptp) cc_final: 0.8378 (tptp) REVERT: C 84 ARG cc_start: 0.8646 (mmp80) cc_final: 0.8250 (mmp80) REVERT: C 89 THR cc_start: 0.8871 (p) cc_final: 0.8644 (p) REVERT: C 129 THR cc_start: 0.8585 (m) cc_final: 0.8380 (p) REVERT: C 165 ARG cc_start: 0.8414 (tpm170) cc_final: 0.8148 (tpm170) REVERT: D 90 MET cc_start: 0.4669 (mmt) cc_final: 0.4017 (tpt) REVERT: D 116 VAL cc_start: 0.8023 (t) cc_final: 0.7775 (t) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1789 time to fit residues: 31.0820 Evaluate side-chains 105 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 0.0570 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 128 GLN A 130 GLN B 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.103464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.093702 restraints weight = 35101.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095195 restraints weight = 23584.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.096261 restraints weight = 17120.082| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4900 Z= 0.189 Angle : 0.709 7.419 6634 Z= 0.357 Chirality : 0.049 0.361 757 Planarity : 0.005 0.061 820 Dihedral : 8.536 56.024 732 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.34), residues: 579 helix: 0.76 (0.36), residues: 213 sheet: -0.77 (0.66), residues: 65 loop : -3.13 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.016 0.001 HIS C 216 PHE 0.027 0.002 PHE D 112 TYR 0.029 0.002 TYR D 117 ARG 0.007 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8570 (mmm) cc_final: 0.7951 (tpt) REVERT: A 46 GLU cc_start: 0.8657 (pp20) cc_final: 0.8393 (pm20) REVERT: A 67 LEU cc_start: 0.8576 (mm) cc_final: 0.8347 (mm) REVERT: A 83 VAL cc_start: 0.8987 (t) cc_final: 0.8567 (t) REVERT: A 125 LEU cc_start: 0.7069 (mt) cc_final: 0.6617 (tp) REVERT: A 135 LYS cc_start: 0.8984 (pttt) cc_final: 0.8081 (tptp) REVERT: A 143 ARG cc_start: 0.7706 (mmm160) cc_final: 0.6113 (ptt180) REVERT: A 156 MET cc_start: 0.7983 (tpt) cc_final: 0.7640 (tpt) REVERT: B 68 PHE cc_start: 0.8600 (p90) cc_final: 0.8271 (p90) REVERT: B 69 ASP cc_start: 0.8201 (m-30) cc_final: 0.7939 (m-30) REVERT: B 70 ILE cc_start: 0.8906 (mt) cc_final: 0.7990 (mp) REVERT: C 84 ARG cc_start: 0.8694 (mmp80) cc_final: 0.8446 (mmp80) REVERT: C 88 CYS cc_start: 0.8892 (m) cc_final: 0.8567 (p) REVERT: D 90 MET cc_start: 0.4616 (mmt) cc_final: 0.3970 (tpt) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1755 time to fit residues: 29.6706 Evaluate side-chains 102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.105064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.095263 restraints weight = 35369.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096688 restraints weight = 23969.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.097786 restraints weight = 17490.818| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4900 Z= 0.160 Angle : 0.720 8.250 6634 Z= 0.355 Chirality : 0.049 0.362 757 Planarity : 0.005 0.057 820 Dihedral : 8.133 55.465 732 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.34), residues: 579 helix: 0.96 (0.36), residues: 212 sheet: -1.16 (0.55), residues: 87 loop : -3.07 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.015 0.001 HIS C 216 PHE 0.034 0.002 PHE B 12 TYR 0.023 0.001 TYR D 117 ARG 0.008 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8612 (mmm) cc_final: 0.7616 (mmm) REVERT: A 46 GLU cc_start: 0.8692 (pp20) cc_final: 0.8402 (pm20) REVERT: A 61 PHE cc_start: 0.8648 (t80) cc_final: 0.8350 (t80) REVERT: A 67 LEU cc_start: 0.8737 (mm) cc_final: 0.8460 (mm) REVERT: A 135 LYS cc_start: 0.8946 (pttt) cc_final: 0.8020 (tptp) REVERT: A 143 ARG cc_start: 0.7640 (mmm160) cc_final: 0.6214 (ptt180) REVERT: A 156 MET cc_start: 0.7866 (tpt) cc_final: 0.7537 (tpt) REVERT: B 19 MET cc_start: 0.7780 (tpt) cc_final: 0.7452 (tpt) REVERT: B 68 PHE cc_start: 0.8238 (p90) cc_final: 0.8027 (p90) REVERT: B 69 ASP cc_start: 0.7980 (m-30) cc_final: 0.7642 (m-30) REVERT: B 70 ILE cc_start: 0.8883 (mt) cc_final: 0.7882 (mp) REVERT: C 89 THR cc_start: 0.8928 (p) cc_final: 0.8714 (p) REVERT: D 90 MET cc_start: 0.4781 (mmt) cc_final: 0.4111 (tpt) REVERT: D 116 VAL cc_start: 0.8045 (t) cc_final: 0.7782 (t) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1783 time to fit residues: 29.2065 Evaluate side-chains 99 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065909 restraints weight = 27021.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067613 restraints weight = 20835.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068911 restraints weight = 16961.323| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4900 Z= 0.220 Angle : 0.737 9.137 6634 Z= 0.367 Chirality : 0.049 0.334 757 Planarity : 0.004 0.032 820 Dihedral : 7.898 54.011 732 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.34), residues: 579 helix: 0.96 (0.36), residues: 216 sheet: -0.85 (0.58), residues: 82 loop : -3.17 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 51 HIS 0.012 0.001 HIS C 216 PHE 0.017 0.002 PHE D 112 TYR 0.031 0.002 TYR D 117 ARG 0.009 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.6523 (p0) cc_final: 0.6314 (p0) REVERT: A 135 LYS cc_start: 0.8989 (pttt) cc_final: 0.8104 (tptp) REVERT: A 143 ARG cc_start: 0.7757 (mmm160) cc_final: 0.6324 (ptt180) REVERT: A 156 MET cc_start: 0.7912 (tpt) cc_final: 0.7572 (tpt) REVERT: B 68 PHE cc_start: 0.8662 (p90) cc_final: 0.8356 (p90) REVERT: B 69 ASP cc_start: 0.8301 (m-30) cc_final: 0.8050 (m-30) REVERT: B 70 ILE cc_start: 0.8915 (mt) cc_final: 0.7944 (mp) REVERT: B 174 TYR cc_start: 0.7151 (t80) cc_final: 0.6820 (t80) REVERT: C 84 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8052 (mmp80) REVERT: C 88 CYS cc_start: 0.9072 (m) cc_final: 0.8687 (p) REVERT: D 90 MET cc_start: 0.4756 (mmt) cc_final: 0.4262 (tpt) REVERT: D 134 TRP cc_start: 0.8179 (m100) cc_final: 0.7907 (m100) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1815 time to fit residues: 29.3459 Evaluate side-chains 104 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.0020 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064911 restraints weight = 28927.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066464 restraints weight = 22221.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067726 restraints weight = 18009.025| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4900 Z= 0.227 Angle : 0.753 8.404 6634 Z= 0.380 Chirality : 0.049 0.326 757 Planarity : 0.005 0.049 820 Dihedral : 7.902 53.885 732 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.34), residues: 579 helix: 0.76 (0.35), residues: 215 sheet: -0.87 (0.57), residues: 87 loop : -3.15 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 51 HIS 0.015 0.001 HIS C 216 PHE 0.038 0.002 PHE B 12 TYR 0.029 0.002 TYR D 117 ARG 0.007 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.6559 (p0) cc_final: 0.6350 (p0) REVERT: A 86 ARG cc_start: 0.6064 (mmm160) cc_final: 0.5855 (mmm160) REVERT: A 135 LYS cc_start: 0.9005 (pttt) cc_final: 0.8134 (tptp) REVERT: A 143 ARG cc_start: 0.7878 (mmm160) cc_final: 0.6448 (ptt180) REVERT: A 156 MET cc_start: 0.7917 (tpt) cc_final: 0.7571 (tpt) REVERT: B 68 PHE cc_start: 0.8657 (p90) cc_final: 0.8316 (p90) REVERT: B 69 ASP cc_start: 0.8368 (m-30) cc_final: 0.8125 (m-30) REVERT: B 70 ILE cc_start: 0.8916 (mt) cc_final: 0.7938 (mp) REVERT: C 84 ARG cc_start: 0.8741 (mmp80) cc_final: 0.7991 (mmp80) REVERT: C 88 CYS cc_start: 0.9052 (m) cc_final: 0.8701 (p) REVERT: D 90 MET cc_start: 0.4778 (mmt) cc_final: 0.4326 (tpt) REVERT: D 134 TRP cc_start: 0.8211 (m100) cc_final: 0.7884 (m100) REVERT: D 136 ILE cc_start: 0.4431 (pt) cc_final: 0.3829 (pt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2037 time to fit residues: 32.0656 Evaluate side-chains 100 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064267 restraints weight = 27233.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065866 restraints weight = 21024.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067126 restraints weight = 17216.784| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4900 Z= 0.203 Angle : 0.756 8.985 6634 Z= 0.379 Chirality : 0.049 0.329 757 Planarity : 0.005 0.047 820 Dihedral : 7.726 53.516 732 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.19 % Allowed : 2.30 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.34), residues: 579 helix: 0.80 (0.35), residues: 215 sheet: -0.86 (0.57), residues: 87 loop : -3.15 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.016 0.002 HIS C 216 PHE 0.027 0.002 PHE D 112 TYR 0.025 0.002 TYR D 117 ARG 0.005 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8796 (mmm) cc_final: 0.7686 (mmm) REVERT: A 46 GLU cc_start: 0.8942 (pp20) cc_final: 0.8603 (tm-30) REVERT: A 99 LEU cc_start: 0.9535 (tt) cc_final: 0.9266 (mm) REVERT: A 135 LYS cc_start: 0.8992 (pttt) cc_final: 0.8068 (tptp) REVERT: A 143 ARG cc_start: 0.7929 (mmm160) cc_final: 0.6528 (ptt180) REVERT: A 156 MET cc_start: 0.7901 (tpt) cc_final: 0.7584 (tpt) REVERT: B 68 PHE cc_start: 0.8646 (p90) cc_final: 0.8368 (p90) REVERT: B 69 ASP cc_start: 0.8359 (m-30) cc_final: 0.8138 (m-30) REVERT: B 70 ILE cc_start: 0.8935 (mt) cc_final: 0.7935 (mt) REVERT: C 84 ARG cc_start: 0.8717 (mmp80) cc_final: 0.8438 (mmp80) REVERT: C 88 CYS cc_start: 0.9127 (m) cc_final: 0.8800 (p) REVERT: D 86 LEU cc_start: 0.7558 (tp) cc_final: 0.7082 (mm) REVERT: D 90 MET cc_start: 0.4878 (mmt) cc_final: 0.4404 (tpt) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2105 time to fit residues: 34.1134 Evaluate side-chains 104 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.0370 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065857 restraints weight = 27116.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.067501 restraints weight = 20855.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068733 restraints weight = 17001.819| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4900 Z= 0.167 Angle : 0.774 9.606 6634 Z= 0.384 Chirality : 0.050 0.340 757 Planarity : 0.005 0.051 820 Dihedral : 7.299 53.857 732 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.35), residues: 579 helix: 1.03 (0.37), residues: 209 sheet: -0.63 (0.59), residues: 86 loop : -3.02 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 157 HIS 0.019 0.001 HIS C 216 PHE 0.032 0.002 PHE B 12 TYR 0.024 0.001 TYR D 117 ARG 0.011 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8815 (mmm) cc_final: 0.7875 (mmm) REVERT: A 46 GLU cc_start: 0.8946 (pp20) cc_final: 0.8622 (pm20) REVERT: A 75 ASP cc_start: 0.6827 (p0) cc_final: 0.6553 (p0) REVERT: A 135 LYS cc_start: 0.8967 (pttt) cc_final: 0.8088 (tptp) REVERT: A 143 ARG cc_start: 0.7992 (mmm160) cc_final: 0.6533 (ptt180) REVERT: A 156 MET cc_start: 0.7967 (tpt) cc_final: 0.7649 (tpt) REVERT: B 70 ILE cc_start: 0.8923 (mt) cc_final: 0.7869 (mt) REVERT: C 84 ARG cc_start: 0.8707 (mmp80) cc_final: 0.8071 (mmp80) REVERT: D 86 LEU cc_start: 0.7651 (tp) cc_final: 0.7229 (mm) REVERT: D 90 MET cc_start: 0.4868 (mmt) cc_final: 0.4271 (tpt) REVERT: D 92 GLN cc_start: 0.8032 (mp10) cc_final: 0.7545 (mp10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2415 time to fit residues: 39.7101 Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063727 restraints weight = 26933.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065327 restraints weight = 20443.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066527 restraints weight = 16542.433| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4900 Z= 0.232 Angle : 0.791 9.067 6634 Z= 0.399 Chirality : 0.050 0.324 757 Planarity : 0.005 0.050 820 Dihedral : 7.340 52.860 732 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.35), residues: 579 helix: 0.82 (0.35), residues: 215 sheet: -0.53 (0.59), residues: 87 loop : -3.12 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 51 HIS 0.019 0.001 HIS C 216 PHE 0.019 0.002 PHE C 94 TYR 0.025 0.002 TYR D 117 ARG 0.006 0.001 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8748 (mmm) cc_final: 0.7817 (mmm) REVERT: A 46 GLU cc_start: 0.8940 (pp20) cc_final: 0.8642 (pm20) REVERT: A 75 ASP cc_start: 0.7112 (p0) cc_final: 0.6859 (p0) REVERT: A 86 ARG cc_start: 0.6240 (mmm160) cc_final: 0.6027 (mmm160) REVERT: A 99 LEU cc_start: 0.9519 (tt) cc_final: 0.9226 (mm) REVERT: A 135 LYS cc_start: 0.8968 (pttt) cc_final: 0.8067 (tptp) REVERT: A 143 ARG cc_start: 0.8089 (mmm160) cc_final: 0.6631 (ptt180) REVERT: A 156 MET cc_start: 0.7997 (tpt) cc_final: 0.7683 (tpt) REVERT: C 84 ARG cc_start: 0.8729 (mmp80) cc_final: 0.8182 (mmp80) REVERT: D 86 LEU cc_start: 0.7653 (tp) cc_final: 0.7264 (mm) REVERT: D 90 MET cc_start: 0.5076 (mmt) cc_final: 0.4503 (tpt) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.2878 time to fit residues: 42.6121 Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064882 restraints weight = 26828.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066507 restraints weight = 20508.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067712 restraints weight = 16709.860| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4900 Z= 0.178 Angle : 0.785 9.719 6634 Z= 0.390 Chirality : 0.050 0.332 757 Planarity : 0.005 0.055 820 Dihedral : 7.093 53.639 732 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.19 % Allowed : 0.38 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.65 (0.35), residues: 579 helix: 0.88 (0.36), residues: 209 sheet: -0.43 (0.60), residues: 86 loop : -3.01 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 157 HIS 0.019 0.001 HIS C 216 PHE 0.028 0.002 PHE B 12 TYR 0.023 0.001 TYR D 117 ARG 0.008 0.001 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.40 seconds wall clock time: 35 minutes 17.63 seconds (2117.63 seconds total)