Starting phenix.real_space_refine on Tue Feb 11 08:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p2p_13171/02_2025/7p2p_13171_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p2p_13171/02_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_13171/02_2025/7p2p_13171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p2p_13171/02_2025/7p2p_13171.map" model { file = "/net/cci-nas-00/data/ceres_data/7p2p_13171/02_2025/7p2p_13171_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p2p_13171/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.23, per 1000 atoms: 0.68 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: 1.21 Conformation dependent library (CDL) restraints added in 593.2 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: 0.47 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: 1.13 Time building geometry restraints manager: 1.41 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- 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 : 0.535 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: 0.2500 time to fit residues: 57.7508 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 : 0.684 ------------------------------------------------------------------------------- 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 = 0.109155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.099276 restraints weight = 34866.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100807 restraints weight = 23613.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101843 restraints weight = 17145.707| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4900 Z= 0.175 Angle : 0.741 8.230 6634 Z= 0.371 Chirality : 0.051 0.438 757 Planarity : 0.005 0.052 820 Dihedral : 9.908 72.391 732 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 : 0.513 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: 0.8403 (m-80) cc_final: 0.7901 (m-80) REVERT: A 24 ASN cc_start: 0.8772 (p0) cc_final: 0.8500 (p0) REVERT: A 75 ASP cc_start: 0.5253 (p0) cc_final: 0.4998 (p0) REVERT: A 135 LYS cc_start: 0.8899 (pttt) cc_final: 0.8155 (tptp) REVERT: A 143 ARG cc_start: 0.7362 (mmm160) cc_final: 0.6019 (ptt180) REVERT: A 156 MET cc_start: 0.8055 (tpt) cc_final: 0.7727 (tpt) REVERT: B 69 ASP cc_start: 0.7553 (m-30) cc_final: 0.7231 (m-30) REVERT: B 70 ILE cc_start: 0.8824 (pt) cc_final: 0.8111 (mp) REVERT: C 84 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8068 (mmp80) REVERT: C 129 THR cc_start: 0.8466 (m) cc_final: 0.8257 (p) REVERT: D 86 LEU cc_start: 0.8029 (mm) cc_final: 0.7713 (tp) REVERT: D 90 MET cc_start: 0.4565 (mmt) cc_final: 0.3884 (tpt) REVERT: D 103 PHE cc_start: 0.8745 (p90) cc_final: 0.8532 (p90) REVERT: D 116 VAL cc_start: 0.8412 (t) cc_final: 0.7764 (t) REVERT: D 150 SER cc_start: 0.8280 (m) cc_final: 0.7887 (t) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.2070 time to fit residues: 37.1433 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 : 0.572 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.108045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098158 restraints weight = 34551.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.099583 restraints weight = 23432.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100595 restraints weight = 17158.165| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4900 Z= 0.161 Angle : 0.723 8.355 6634 Z= 0.357 Chirality : 0.050 0.396 757 Planarity : 0.005 0.083 820 Dihedral : 9.195 64.904 732 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: -2.15 (0.33), residues: 579 helix: 0.54 (0.36), residues: 212 sheet: -0.86 (0.61), residues: 68 loop : -3.22 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.015 0.001 HIS C 216 PHE 0.030 0.002 PHE B 12 TYR 0.024 0.001 TYR D 117 ARG 0.006 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 141 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 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 40 MET cc_start: 0.8512 (mmm) cc_final: 0.8174 (tpt) REVERT: A 46 GLU cc_start: 0.8656 (pp20) cc_final: 0.8344 (pm20) REVERT: A 61 PHE cc_start: 0.8540 (t80) cc_final: 0.8243 (t80) REVERT: A 67 LEU cc_start: 0.8565 (mm) cc_final: 0.8342 (mm) REVERT: A 75 ASP cc_start: 0.5555 (p0) cc_final: 0.5343 (p0) REVERT: A 135 LYS cc_start: 0.8905 (pttt) cc_final: 0.8130 (tptp) REVERT: A 143 ARG cc_start: 0.7366 (mmm160) cc_final: 0.6091 (ptt180) REVERT: A 156 MET cc_start: 0.8026 (tpt) cc_final: 0.7706 (tpt) REVERT: B 69 ASP cc_start: 0.7918 (m-30) cc_final: 0.7485 (m-30) REVERT: B 96 LYS cc_start: 0.8666 (tptp) cc_final: 0.8376 (tptp) REVERT: C 89 THR cc_start: 0.8831 (p) cc_final: 0.8608 (p) REVERT: C 165 ARG cc_start: 0.8416 (tpm170) cc_final: 0.8138 (tpm170) REVERT: D 90 MET cc_start: 0.4664 (mmt) cc_final: 0.4001 (tpt) REVERT: D 116 VAL cc_start: 0.8003 (t) cc_final: 0.7744 (t) REVERT: D 150 SER cc_start: 0.8170 (m) cc_final: 0.7930 (t) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1814 time to fit residues: 31.6526 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 : 0.568 ------------------------------------------------------------------------------- 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: 9.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 23 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 B 76 ASN C 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.107983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097955 restraints weight = 35124.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.099491 restraints weight = 23415.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.100504 restraints weight = 16905.573| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4900 Z= 0.155 Angle : 0.706 9.495 6634 Z= 0.351 Chirality : 0.049 0.381 757 Planarity : 0.005 0.079 820 Dihedral : 8.363 56.348 732 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 4.80 % 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: -1.94 (0.34), residues: 579 helix: 0.75 (0.36), residues: 213 sheet: -1.05 (0.59), residues: 77 loop : -3.10 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 148 HIS 0.015 0.001 HIS C 216 PHE 0.029 0.001 PHE D 112 TYR 0.027 0.001 TYR D 117 ARG 0.009 0.001 ARG B 112 *********************** 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 136 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.573 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 67 LEU cc_start: 0.8509 (mm) cc_final: 0.8281 (mm) REVERT: A 135 LYS cc_start: 0.8950 (pttt) cc_final: 0.8050 (tptp) REVERT: A 143 ARG cc_start: 0.7444 (mmm160) cc_final: 0.5994 (ptt180) REVERT: A 156 MET cc_start: 0.7976 (tpt) cc_final: 0.7640 (tpt) REVERT: B 68 PHE cc_start: 0.8522 (p90) cc_final: 0.8219 (p90) REVERT: B 69 ASP cc_start: 0.8074 (m-30) cc_final: 0.7828 (m-30) REVERT: B 70 ILE cc_start: 0.8848 (mt) cc_final: 0.7967 (mp) REVERT: B 96 LYS cc_start: 0.8620 (tptp) cc_final: 0.8340 (tptp) REVERT: C 84 ARG cc_start: 0.8584 (mmp80) cc_final: 0.7916 (mmp80) REVERT: C 88 CYS cc_start: 0.8881 (m) cc_final: 0.8450 (p) REVERT: C 165 ARG cc_start: 0.8399 (tpm170) cc_final: 0.8125 (tpm170) REVERT: D 90 MET cc_start: 0.4496 (mmt) cc_final: 0.3840 (tpt) REVERT: D 116 VAL cc_start: 0.8042 (t) cc_final: 0.7832 (t) REVERT: D 150 SER cc_start: 0.8340 (m) cc_final: 0.7980 (t) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1791 time to fit residues: 30.1313 Evaluate side-chains 110 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092860 restraints weight = 35456.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094326 restraints weight = 23557.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095351 restraints weight = 17069.082| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4900 Z= 0.214 Angle : 0.733 6.679 6634 Z= 0.371 Chirality : 0.049 0.344 757 Planarity : 0.005 0.050 820 Dihedral : 8.092 54.588 732 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.19 % Allowed : 4.22 % Favored : 95.59 % 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: -1.84 (0.34), residues: 579 helix: 0.86 (0.36), residues: 212 sheet: -0.94 (0.58), residues: 80 loop : -3.09 (0.33), residues: 287 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 0.034 0.002 PHE D 91 TYR 0.030 0.002 TYR D 117 ARG 0.019 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 135 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.546 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: 0.8535 (mmm) cc_final: 0.8246 (mmm) REVERT: A 75 ASP cc_start: 0.5961 (p0) cc_final: 0.5748 (p0) REVERT: A 135 LYS cc_start: 0.8948 (pttt) cc_final: 0.8130 (tptp) REVERT: A 143 ARG cc_start: 0.7688 (mmm160) cc_final: 0.6155 (ptt180) REVERT: A 156 MET cc_start: 0.7946 (tpt) cc_final: 0.7593 (tpt) REVERT: B 68 PHE cc_start: 0.8701 (p90) cc_final: 0.8403 (p90) REVERT: B 70 ILE cc_start: 0.8915 (mt) cc_final: 0.7980 (mp) REVERT: C 84 ARG cc_start: 0.8698 (mmp80) cc_final: 0.8034 (mmp80) REVERT: D 90 MET cc_start: 0.4724 (mmt) cc_final: 0.4168 (tpt) REVERT: D 134 TRP cc_start: 0.7977 (m100) cc_final: 0.7512 (m100) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1827 time to fit residues: 31.0652 Evaluate side-chains 103 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.0770 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.085957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068955 restraints weight = 26546.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070654 restraints weight = 20519.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071941 restraints weight = 16777.931| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4976 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= 0.165 Angle : 0.715 8.105 6634 Z= 0.352 Chirality : 0.048 0.350 757 Planarity : 0.004 0.042 820 Dihedral : 7.777 55.096 732 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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: -1.61 (0.35), residues: 579 helix: 1.11 (0.36), residues: 210 sheet: -0.64 (0.59), residues: 80 loop : -3.05 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.017 0.001 HIS C 216 PHE 0.026 0.002 PHE D 112 TYR 0.024 0.001 TYR D 117 ARG 0.008 0.001 ARG A 86 *********************** 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: 1 poor density : 128 time to evaluate : 0.500 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: 0.8538 (mmm) cc_final: 0.7821 (mmm) REVERT: A 46 GLU cc_start: 0.8790 (pp20) cc_final: 0.8474 (pm20) REVERT: A 67 LEU cc_start: 0.8366 (mm) cc_final: 0.8074 (mm) REVERT: A 135 LYS cc_start: 0.8972 (pttt) cc_final: 0.8102 (tptp) REVERT: A 143 ARG cc_start: 0.7555 (mmm160) cc_final: 0.6156 (ptt180) REVERT: A 156 MET cc_start: 0.7919 (tpt) cc_final: 0.7593 (tpt) REVERT: B 68 PHE cc_start: 0.8554 (p90) cc_final: 0.8330 (p90) REVERT: B 70 ILE cc_start: 0.8882 (mt) cc_final: 0.7886 (mp) REVERT: C 84 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8170 (mmp80) REVERT: C 88 CYS cc_start: 0.9035 (m) cc_final: 0.8602 (p) REVERT: D 90 MET cc_start: 0.4754 (mmt) cc_final: 0.4244 (tpt) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1758 time to fit residues: 28.2311 Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.082735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067723 restraints weight = 28252.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069319 restraints weight = 21835.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070560 restraints weight = 17786.617| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5216 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= 0.184 Angle : 0.709 7.007 6634 Z= 0.357 Chirality : 0.048 0.342 757 Planarity : 0.004 0.031 820 Dihedral : 7.506 54.122 732 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -1.66 (0.35), residues: 579 helix: 1.02 (0.36), residues: 211 sheet: -0.68 (0.59), residues: 82 loop : -3.06 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.017 0.001 HIS C 216 PHE 0.020 0.002 PHE D 112 TYR 0.026 0.002 TYR D 117 ARG 0.009 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 : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8631 (mmm) cc_final: 0.8344 (mmm) REVERT: A 86 ARG cc_start: 0.6033 (mmm160) cc_final: 0.5813 (mmm160) REVERT: A 135 LYS cc_start: 0.8997 (pttt) cc_final: 0.8074 (tptp) REVERT: A 143 ARG cc_start: 0.7710 (mmm160) cc_final: 0.6311 (ptt180) REVERT: A 156 MET cc_start: 0.7934 (tpt) cc_final: 0.7598 (tpt) REVERT: C 84 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8098 (mmp80) REVERT: D 90 MET cc_start: 0.4895 (mmt) cc_final: 0.4368 (tpt) REVERT: D 134 TRP cc_start: 0.8091 (m100) cc_final: 0.7540 (m100) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1881 time to fit residues: 29.5005 Evaluate side-chains 95 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS C 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.084718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068670 restraints weight = 27815.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070292 restraints weight = 21498.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.071543 restraints weight = 17565.517| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4900 Z= 0.167 Angle : 0.714 7.171 6634 Z= 0.357 Chirality : 0.048 0.344 757 Planarity : 0.004 0.033 820 Dihedral : 7.259 54.348 732 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.19 % Allowed : 1.34 % Favored : 98.46 % 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: -1.56 (0.35), residues: 579 helix: 1.09 (0.36), residues: 209 sheet: -0.51 (0.59), residues: 82 loop : -3.00 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.017 0.001 HIS C 216 PHE 0.029 0.002 PHE D 112 TYR 0.023 0.001 TYR D 117 ARG 0.005 0.000 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 133 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8610 (mmm) cc_final: 0.7591 (mmm) REVERT: A 67 LEU cc_start: 0.8429 (mm) cc_final: 0.8151 (mm) REVERT: A 86 ARG cc_start: 0.6001 (mmm160) cc_final: 0.5784 (mmm160) REVERT: A 135 LYS cc_start: 0.8990 (pttt) cc_final: 0.8075 (tptp) REVERT: A 143 ARG cc_start: 0.7683 (mmm160) cc_final: 0.6274 (ptt180) REVERT: A 156 MET cc_start: 0.7916 (tpt) cc_final: 0.7584 (tpt) REVERT: B 65 PHE cc_start: 0.7235 (m-80) cc_final: 0.6992 (m-80) REVERT: C 84 ARG cc_start: 0.8635 (mmp80) cc_final: 0.8090 (mmp80) REVERT: C 88 CYS cc_start: 0.9029 (m) cc_final: 0.8601 (p) REVERT: D 90 MET cc_start: 0.4788 (mmt) cc_final: 0.4309 (tpt) REVERT: D 134 TRP cc_start: 0.8062 (m100) cc_final: 0.7514 (m100) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.2200 time to fit residues: 38.3129 Evaluate side-chains 99 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.081970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066672 restraints weight = 27800.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068245 restraints weight = 21461.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069415 restraints weight = 17527.891| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4900 Z= 0.184 Angle : 0.737 8.808 6634 Z= 0.368 Chirality : 0.048 0.338 757 Planarity : 0.005 0.057 820 Dihedral : 7.090 53.512 732 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % 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: -1.60 (0.35), residues: 579 helix: 1.07 (0.36), residues: 211 sheet: -0.44 (0.60), residues: 82 loop : -3.09 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 51 HIS 0.018 0.001 HIS C 216 PHE 0.026 0.002 PHE D 112 TYR 0.026 0.002 TYR D 117 ARG 0.006 0.000 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: 0 poor density : 131 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.6736 (p0) cc_final: 0.6524 (p0) REVERT: A 86 ARG cc_start: 0.5949 (mmm160) cc_final: 0.5728 (mmm160) REVERT: A 135 LYS cc_start: 0.8975 (pttt) cc_final: 0.8037 (tptp) REVERT: A 143 ARG cc_start: 0.7758 (mmm160) cc_final: 0.6410 (ptt180) REVERT: A 156 MET cc_start: 0.7932 (tpt) cc_final: 0.7632 (tpt) REVERT: B 65 PHE cc_start: 0.7277 (m-80) cc_final: 0.7040 (m-80) REVERT: B 174 TYR cc_start: 0.7124 (t80) cc_final: 0.6837 (t80) REVERT: C 84 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8366 (mmp80) REVERT: D 90 MET cc_start: 0.4843 (mmt) cc_final: 0.4362 (tpt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1791 time to fit residues: 29.6031 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 : 0.594 ------------------------------------------------------------------------------- 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: 7.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066075 restraints weight = 28121.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067564 restraints weight = 21895.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068698 restraints weight = 17928.031| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4900 Z= 0.200 Angle : 0.758 9.127 6634 Z= 0.383 Chirality : 0.049 0.334 757 Planarity : 0.005 0.051 820 Dihedral : 7.093 53.236 732 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % 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: -1.61 (0.35), residues: 579 helix: 0.94 (0.36), residues: 217 sheet: -0.36 (0.61), residues: 82 loop : -3.11 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 51 HIS 0.021 0.002 HIS C 216 PHE 0.023 0.002 PHE B 24 TYR 0.024 0.002 TYR D 117 ARG 0.005 0.001 ARG A 90 ********************** 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 133 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.535 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: 0.8666 (mmm) cc_final: 0.7729 (mmm) REVERT: A 53 LEU cc_start: 0.7254 (tp) cc_final: 0.6841 (pp) REVERT: A 135 LYS cc_start: 0.8975 (pttt) cc_final: 0.8044 (tptp) REVERT: A 143 ARG cc_start: 0.7907 (mmm160) cc_final: 0.6573 (ptt180) REVERT: A 156 MET cc_start: 0.7955 (tpt) cc_final: 0.7670 (tpt) REVERT: B 129 PHE cc_start: 0.8224 (t80) cc_final: 0.8000 (t80) REVERT: B 174 TYR cc_start: 0.7302 (t80) cc_final: 0.7023 (t80) REVERT: C 84 ARG cc_start: 0.8704 (mmp80) cc_final: 0.8401 (mmp80) REVERT: D 90 MET cc_start: 0.4948 (mmt) cc_final: 0.4483 (tpt) REVERT: D 136 ILE cc_start: 0.4413 (pt) cc_final: 0.4069 (pt) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1829 time to fit residues: 30.4370 Evaluate side-chains 103 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067073 restraints weight = 27054.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068700 restraints weight = 20811.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.069980 restraints weight = 16967.509| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5928 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= 0.169 Angle : 0.756 9.651 6634 Z= 0.377 Chirality : 0.048 0.340 757 Planarity : 0.005 0.051 820 Dihedral : 6.900 53.618 732 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % 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: -1.47 (0.35), residues: 579 helix: 1.12 (0.36), residues: 211 sheet: -0.36 (0.61), residues: 82 loop : -2.97 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 144 HIS 0.018 0.001 HIS C 216 PHE 0.021 0.002 PHE D 112 TYR 0.023 0.001 TYR D 117 ARG 0.010 0.001 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.69 seconds wall clock time: 30 minutes 56.28 seconds (1856.28 seconds total)