Starting phenix.real_space_refine on Mon Sep 23 19:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_13171_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_13171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_13171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_13171_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2p_13171/09_2024/7p2p_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-5461/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: 3.45, per 1000 atoms: 0.72 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: 1.46 Conformation dependent library (CDL) restraints added in 548.8 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: 0.51 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: 0.98 Time building geometry restraints manager: 1.47 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: 0.470 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.080 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.547 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: 0.2365 time to fit residues: 54.6296 Evaluate side-chains 109 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.575 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: 0.8659 (m-80) cc_final: 0.8216 (m-80) REVERT: A 24 ASN cc_start: 0.8778 (p0) cc_final: 0.8494 (p0) REVERT: A 75 ASP cc_start: 0.5286 (p0) cc_final: 0.5036 (p0) REVERT: A 135 LYS cc_start: 0.8882 (pttt) cc_final: 0.8132 (tptp) REVERT: A 143 ARG cc_start: 0.7618 (mmm160) cc_final: 0.6177 (ptt180) REVERT: A 156 MET cc_start: 0.8141 (tpt) cc_final: 0.7772 (tpt) REVERT: B 69 ASP cc_start: 0.7396 (m-30) cc_final: 0.6956 (m-30) REVERT: B 70 ILE cc_start: 0.8828 (pt) cc_final: 0.8103 (mp) REVERT: C 84 ARG cc_start: 0.8696 (mmp80) cc_final: 0.8139 (mmp80) REVERT: D 86 LEU cc_start: 0.8000 (mm) cc_final: 0.7747 (tp) REVERT: D 90 MET cc_start: 0.4542 (mmt) cc_final: 0.3946 (tpt) REVERT: D 116 VAL cc_start: 0.8251 (t) cc_final: 0.7628 (t) REVERT: D 150 SER cc_start: 0.8338 (m) cc_final: 0.7948 (t) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.1999 time to fit residues: 35.8603 Evaluate side-chains 110 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4900 Z= 0.178 Angle : 0.724 8.786 6634 Z= 0.360 Chirality : 0.050 0.389 757 Planarity : 0.005 0.083 820 Dihedral : 9.241 64.843 732 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -2.17 (0.33), residues: 579 helix: 0.51 (0.36), residues: 212 sheet: -0.87 (0.61), residues: 68 loop : -3.23 (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 0.025 0.002 TYR D 117 ARG 0.007 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 137 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.553 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: 0.8327 (t80) cc_final: 0.8055 (t80) REVERT: A 67 LEU cc_start: 0.8886 (mm) cc_final: 0.8633 (mm) REVERT: A 135 LYS cc_start: 0.8869 (pttt) cc_final: 0.8054 (tptp) REVERT: A 143 ARG cc_start: 0.7686 (mmm160) cc_final: 0.6261 (ptt180) REVERT: A 156 MET cc_start: 0.8053 (tpt) cc_final: 0.7709 (tpt) REVERT: B 69 ASP cc_start: 0.7621 (m-30) cc_final: 0.7254 (m-30) REVERT: B 96 LYS cc_start: 0.8548 (tptp) cc_final: 0.8256 (tptp) REVERT: C 89 THR cc_start: 0.8882 (p) cc_final: 0.8658 (p) REVERT: C 165 ARG cc_start: 0.8441 (tpm170) cc_final: 0.8223 (tpm170) REVERT: D 90 MET cc_start: 0.4718 (mmt) cc_final: 0.4103 (tpt) REVERT: D 116 VAL cc_start: 0.7840 (t) cc_final: 0.7609 (t) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1796 time to fit residues: 30.4730 Evaluate side-chains 104 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4843 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= 0.251 Angle : 0.764 9.590 6634 Z= 0.389 Chirality : 0.050 0.344 757 Planarity : 0.005 0.055 820 Dihedral : 8.879 57.451 732 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % 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: -2.08 (0.34), residues: 579 helix: 0.60 (0.35), residues: 213 sheet: -0.84 (0.66), residues: 68 loop : -3.19 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 51 HIS 0.016 0.002 HIS C 216 PHE 0.032 0.002 PHE D 112 TYR 0.031 0.002 TYR D 117 ARG 0.010 0.001 ARG A 141 *********************** 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 130 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.555 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 135 LYS cc_start: 0.8919 (pttt) cc_final: 0.8095 (tptp) REVERT: A 143 ARG cc_start: 0.8087 (mmm160) cc_final: 0.6460 (ptt180) REVERT: A 156 MET cc_start: 0.8006 (tpt) cc_final: 0.7625 (tpt) REVERT: B 69 ASP cc_start: 0.7892 (m-30) cc_final: 0.7482 (m-30) REVERT: B 70 ILE cc_start: 0.8927 (mt) cc_final: 0.7898 (mp) REVERT: C 84 ARG cc_start: 0.8684 (mmp80) cc_final: 0.7781 (mmp80) REVERT: C 186 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6989 (tm-30) REVERT: D 90 MET cc_start: 0.4751 (mmt) cc_final: 0.4270 (tpt) REVERT: D 116 VAL cc_start: 0.7920 (t) cc_final: 0.7578 (t) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1803 time to fit residues: 29.0793 Evaluate side-chains 102 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5365 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= 0.217 Angle : 0.748 8.858 6634 Z= 0.377 Chirality : 0.050 0.339 757 Planarity : 0.005 0.049 820 Dihedral : 8.692 55.221 732 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % 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: -1.97 (0.34), residues: 579 helix: 0.73 (0.35), residues: 216 sheet: -1.07 (0.56), residues: 87 loop : -3.23 (0.33), residues: 276 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 0.015 0.002 PHE D 103 TYR 0.027 0.002 TYR D 117 ARG 0.007 0.001 ARG A 90 *********************** 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 fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8859 (mmm) cc_final: 0.8562 (mmm) REVERT: A 135 LYS cc_start: 0.8941 (pttt) cc_final: 0.8076 (tptp) REVERT: A 143 ARG cc_start: 0.8049 (mmm160) cc_final: 0.6568 (ptt180) REVERT: A 156 MET cc_start: 0.7961 (tpt) cc_final: 0.7584 (tpt) REVERT: B 69 ASP cc_start: 0.8119 (m-30) cc_final: 0.7694 (m-30) REVERT: C 84 ARG cc_start: 0.8613 (mmp80) cc_final: 0.7877 (mmp80) REVERT: C 88 CYS cc_start: 0.8906 (m) cc_final: 0.8532 (p) REVERT: D 86 LEU cc_start: 0.7549 (tp) cc_final: 0.6970 (mm) REVERT: D 90 MET cc_start: 0.4921 (mmt) cc_final: 0.4312 (tpt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1718 time to fit residues: 27.8756 Evaluate side-chains 100 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- 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 76 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5508 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= 0.177 Angle : 0.720 10.726 6634 Z= 0.357 Chirality : 0.049 0.347 757 Planarity : 0.005 0.041 820 Dihedral : 8.251 54.460 732 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -1.79 (0.35), residues: 579 helix: 0.93 (0.35), residues: 216 sheet: -0.88 (0.57), residues: 87 loop : -3.21 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.016 0.001 HIS C 216 PHE 0.021 0.002 PHE D 112 TYR 0.026 0.001 TYR D 117 ARG 0.007 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 125 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8812 (tmm) cc_final: 0.8598 (tmm) REVERT: A 135 LYS cc_start: 0.8904 (pttt) cc_final: 0.8046 (tptp) REVERT: A 143 ARG cc_start: 0.8052 (mmm160) cc_final: 0.6577 (ptt180) REVERT: A 156 MET cc_start: 0.7973 (tpt) cc_final: 0.7600 (tpt) REVERT: B 69 ASP cc_start: 0.7836 (m-30) cc_final: 0.7586 (m-30) REVERT: C 84 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8195 (mmp80) REVERT: C 88 CYS cc_start: 0.8918 (m) cc_final: 0.8608 (p) REVERT: C 165 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8751 (tpp-160) REVERT: D 86 LEU cc_start: 0.7557 (tp) cc_final: 0.7025 (mm) REVERT: D 90 MET cc_start: 0.4968 (mmt) cc_final: 0.4352 (tpt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1839 time to fit residues: 28.3912 Evaluate side-chains 100 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5655 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= 0.171 Angle : 0.723 9.357 6634 Z= 0.361 Chirality : 0.049 0.348 757 Planarity : 0.005 0.047 820 Dihedral : 7.819 54.157 732 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -1.73 (0.35), residues: 579 helix: 1.03 (0.36), residues: 209 sheet: -0.79 (0.58), residues: 86 loop : -3.13 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.017 0.001 HIS C 216 PHE 0.018 0.002 PHE D 112 TYR 0.026 0.001 TYR D 117 ARG 0.008 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 127 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8752 (tmm) cc_final: 0.8522 (tmm) REVERT: A 40 MET cc_start: 0.8985 (mmm) cc_final: 0.8767 (mmm) REVERT: A 75 ASP cc_start: 0.6389 (p0) cc_final: 0.6153 (p0) REVERT: A 135 LYS cc_start: 0.8903 (pttt) cc_final: 0.7991 (tptp) REVERT: A 143 ARG cc_start: 0.8022 (mmm160) cc_final: 0.6569 (ptt180) REVERT: A 156 MET cc_start: 0.7957 (tpt) cc_final: 0.7583 (tpt) REVERT: B 68 PHE cc_start: 0.7929 (p90) cc_final: 0.7639 (p90) REVERT: B 69 ASP cc_start: 0.7963 (m-30) cc_final: 0.7616 (m-30) REVERT: C 84 ARG cc_start: 0.8602 (mmp80) cc_final: 0.7850 (mmp80) REVERT: C 88 CYS cc_start: 0.8900 (m) cc_final: 0.8599 (p) REVERT: C 158 GLN cc_start: 0.7200 (pm20) cc_final: 0.6869 (pm20) REVERT: C 165 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8784 (tpp-160) REVERT: D 86 LEU cc_start: 0.7558 (tp) cc_final: 0.7080 (mm) REVERT: D 90 MET cc_start: 0.4896 (mmt) cc_final: 0.4329 (tpt) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1777 time to fit residues: 28.0085 Evaluate side-chains 100 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5909 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= 0.202 Angle : 0.758 10.519 6634 Z= 0.384 Chirality : 0.049 0.340 757 Planarity : 0.005 0.046 820 Dihedral : 7.655 53.803 732 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 (0.35), residues: 579 helix: 0.83 (0.36), residues: 215 sheet: -0.72 (0.60), residues: 86 loop : -3.24 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 51 HIS 0.018 0.001 HIS C 216 PHE 0.030 0.002 PHE D 112 TYR 0.025 0.002 TYR D 117 ARG 0.009 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 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8733 (tmm) cc_final: 0.8521 (tmm) REVERT: A 40 MET cc_start: 0.8949 (mmm) cc_final: 0.7716 (mmm) REVERT: A 135 LYS cc_start: 0.8893 (pttt) cc_final: 0.8034 (tptp) REVERT: A 143 ARG cc_start: 0.8125 (mmm160) cc_final: 0.6663 (ptt180) REVERT: A 156 MET cc_start: 0.7987 (tpt) cc_final: 0.7617 (tpt) REVERT: B 68 PHE cc_start: 0.7976 (p90) cc_final: 0.7694 (p90) REVERT: B 69 ASP cc_start: 0.7990 (m-30) cc_final: 0.7743 (m-30) REVERT: C 84 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8209 (mmp80) REVERT: C 88 CYS cc_start: 0.8905 (m) cc_final: 0.8217 (p) REVERT: C 92 CYS cc_start: 0.9081 (m) cc_final: 0.8854 (m) REVERT: C 158 GLN cc_start: 0.7048 (pm20) cc_final: 0.6753 (pm20) REVERT: C 165 ARG cc_start: 0.8995 (ttp-110) cc_final: 0.8778 (tpp-160) REVERT: D 86 LEU cc_start: 0.7673 (tp) cc_final: 0.7196 (mm) REVERT: D 90 MET cc_start: 0.5083 (mmt) cc_final: 0.4429 (tpt) REVERT: D 136 ILE cc_start: 0.3982 (pt) cc_final: 0.3413 (pt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1764 time to fit residues: 27.7952 Evaluate side-chains 100 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0030 chunk 36 optimal weight: 0.0770 chunk 55 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.6064 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= 0.167 Angle : 0.757 10.396 6634 Z= 0.377 Chirality : 0.049 0.346 757 Planarity : 0.005 0.045 820 Dihedral : 7.360 54.315 732 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % 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: -1.69 (0.35), residues: 579 helix: 1.00 (0.37), residues: 209 sheet: -0.68 (0.60), residues: 86 loop : -3.08 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 144 HIS 0.018 0.001 HIS C 216 PHE 0.017 0.001 PHE C 94 TYR 0.022 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 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8666 (tmm) cc_final: 0.8462 (tmm) REVERT: A 40 MET cc_start: 0.9021 (mmm) cc_final: 0.7808 (mmm) REVERT: A 46 GLU cc_start: 0.8897 (pp20) cc_final: 0.8599 (pm20) REVERT: A 75 ASP cc_start: 0.6548 (p0) cc_final: 0.6331 (p0) REVERT: A 135 LYS cc_start: 0.8912 (pttt) cc_final: 0.7989 (tptp) REVERT: A 143 ARG cc_start: 0.8040 (mmm160) cc_final: 0.6629 (ptt180) REVERT: A 156 MET cc_start: 0.7989 (tpt) cc_final: 0.7624 (tpt) REVERT: C 84 ARG cc_start: 0.8523 (mmp80) cc_final: 0.7808 (mmp80) REVERT: C 88 CYS cc_start: 0.8880 (m) cc_final: 0.8545 (p) REVERT: C 89 THR cc_start: 0.9002 (p) cc_final: 0.8800 (p) REVERT: C 158 GLN cc_start: 0.7125 (pm20) cc_final: 0.6828 (pm20) REVERT: D 86 LEU cc_start: 0.7707 (tp) cc_final: 0.7254 (mm) REVERT: D 90 MET cc_start: 0.4912 (mmt) cc_final: 0.4288 (tpt) REVERT: D 116 VAL cc_start: 0.7738 (t) cc_final: 0.7473 (t) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1818 time to fit residues: 29.2068 Evaluate side-chains 100 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4900 Z= 0.291 Angle : 0.838 9.378 6634 Z= 0.428 Chirality : 0.050 0.322 757 Planarity : 0.006 0.054 820 Dihedral : 7.755 52.628 732 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % 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: -2.02 (0.34), residues: 579 helix: 0.53 (0.34), residues: 215 sheet: -0.80 (0.59), residues: 88 loop : -3.22 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 51 HIS 0.021 0.002 HIS C 216 PHE 0.018 0.002 PHE C 94 TYR 0.031 0.003 TYR D 117 ARG 0.004 0.001 ARG C 214 ********************** 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 117 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9072 (mmm) cc_final: 0.8774 (mmm) REVERT: A 46 GLU cc_start: 0.8994 (pp20) cc_final: 0.8791 (pm20) REVERT: A 135 LYS cc_start: 0.8946 (pttt) cc_final: 0.7936 (tptp) REVERT: A 143 ARG cc_start: 0.8361 (mmm160) cc_final: 0.6940 (ptt180) REVERT: A 156 MET cc_start: 0.8090 (tpt) cc_final: 0.7719 (tpt) REVERT: B 68 PHE cc_start: 0.7921 (p90) cc_final: 0.7605 (p90) REVERT: C 84 ARG cc_start: 0.8649 (mmp80) cc_final: 0.8106 (mmp80) REVERT: C 88 CYS cc_start: 0.8982 (m) cc_final: 0.8664 (p) REVERT: D 90 MET cc_start: 0.5172 (mmt) cc_final: 0.4601 (tpt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1771 time to fit residues: 25.8070 Evaluate side-chains 90 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0070 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.079441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065435 restraints weight = 29750.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066881 restraints weight = 23055.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067990 restraints weight = 18893.630| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4900 Z= 0.186 Angle : 0.791 8.365 6634 Z= 0.393 Chirality : 0.050 0.340 757 Planarity : 0.005 0.058 820 Dihedral : 7.264 53.959 732 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % 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: -1.98 (0.34), residues: 579 helix: 0.72 (0.35), residues: 209 sheet: -0.92 (0.63), residues: 78 loop : -3.13 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 51 HIS 0.018 0.001 HIS C 216 PHE 0.017 0.002 PHE C 94 TYR 0.028 0.002 TYR C 121 ARG 0.006 0.001 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.60 seconds wall clock time: 25 minutes 16.47 seconds (1516.47 seconds total)