Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.map" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7dnj_30785.pdb" } resolution = 3.3 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.119 sd= 0.276 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: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 1736 2.51 5 N 472 2.21 5 O 535 1.98 5 H 2800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5551 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3184 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1174 Classifications: {'peptide': 72} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.89, per 1000 atoms: 0.34 Number of scatterers: 5551 At special positions: 0 Unit cell: (67.925, 71.06, 110.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 535 8.00 N 472 7.00 C 1736 6.00 H 2800 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 325.8 milliseconds Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 50.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.570A pdb=" N SER A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.582A pdb=" N ALA A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.893A pdb=" N TYR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 128 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 140 removed outlier: 5.080A pdb=" N ASP A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.760A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 removed outlier: 3.500A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.502A pdb=" N GLN A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'H' and resid 23 through 33 Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 56 through 59 No H-bonds generated for 'chain 'H' and resid 56 through 59' Processing sheet with id= A, first strand: chain 'E' and resid 12 through 16 removed outlier: 3.522A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.721A pdb=" N ILE H 3 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER H 65 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS H 6 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU H 67 " --> pdb=" O LYS H 6 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 333 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: 1.60 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 2798 1.14 - 1.31: 487 1.31 - 1.47: 1016 1.47 - 1.64: 1275 1.64 - 1.80: 14 Bond restraints: 5590 Sorted by residual: bond pdb=" NE2 GLN E 49 " pdb="HE21 GLN E 49 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N LEU E 67 " pdb=" H LEU E 67 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N ILE E 13 " pdb=" H ILE E 13 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" NE ARG A 93 " pdb=" HE ARG A 93 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ALA A 110 " pdb=" H ALA A 110 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 5585 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.82: 85 106.82 - 113.59: 6828 113.59 - 120.36: 1789 120.36 - 127.13: 1425 127.13 - 133.90: 24 Bond angle restraints: 10151 Sorted by residual: angle pdb=" N GLY A 54 " pdb=" CA GLY A 54 " pdb=" C GLY A 54 " ideal model delta sigma weight residual 112.65 115.10 -2.45 1.30e+00 5.92e-01 3.56e+00 angle pdb=" C SER A 53 " pdb=" N GLY A 54 " pdb=" CA GLY A 54 " ideal model delta sigma weight residual 121.87 118.84 3.03 1.64e+00 3.72e-01 3.42e+00 angle pdb=" N GLY H 35 " pdb=" CA GLY H 35 " pdb=" C GLY H 35 " ideal model delta sigma weight residual 113.18 116.85 -3.67 2.37e+00 1.78e-01 2.39e+00 angle pdb=" C VAL E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta sigma weight residual 122.93 120.74 2.19 1.45e+00 4.76e-01 2.28e+00 angle pdb=" C GLU H 64 " pdb=" CA GLU H 64 " pdb=" CB GLU H 64 " ideal model delta sigma weight residual 111.80 109.78 2.02 1.46e+00 4.69e-01 1.91e+00 ... (remaining 10146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1667 15.91 - 31.81: 191 31.81 - 47.72: 41 47.72 - 63.62: 29 63.62 - 79.53: 6 Dihedral angle restraints: 1934 sinusoidal: 1470 harmonic: 464 Sorted by residual: dihedral pdb=" CB LYS E 33 " pdb=" CG LYS E 33 " pdb=" CD LYS E 33 " pdb=" CE LYS E 33 " ideal model delta sinusoidal sigma weight residual -60.00 -116.56 56.56 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA GLN H 41 " pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " pdb=" CD GLN H 41 " ideal model delta sinusoidal sigma weight residual 60.00 113.52 -53.52 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA GLN H 41 " pdb=" C GLN H 41 " pdb=" N ARG H 42 " pdb=" CA ARG H 42 " ideal model delta harmonic sigma weight residual 180.00 165.24 14.76 0 5.00e+00 4.00e-02 8.71e+00 ... (remaining 1931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 272 0.028 - 0.056: 110 0.056 - 0.084: 36 0.084 - 0.112: 15 0.112 - 0.140: 8 Chirality restraints: 441 Sorted by residual: chirality pdb=" CA ILE E 44 " pdb=" N ILE E 44 " pdb=" C ILE E 44 " pdb=" CB ILE E 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE H 36 " pdb=" N ILE H 36 " pdb=" C ILE H 36 " pdb=" CB ILE H 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE E 13 " pdb=" N ILE E 13 " pdb=" C ILE E 13 " pdb=" CB ILE E 13 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 438 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 30 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 122 " 0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 123 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 37 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.51e-01 pdb=" N PRO E 38 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.011 5.00e-02 4.00e+02 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 453 2.14 - 2.76: 10394 2.76 - 3.37: 16013 3.37 - 3.99: 21305 3.99 - 4.60: 31691 Nonbonded interactions: 79856 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 23 " pdb=" OE1 GLU A 60 " model vdw 1.530 1.850 nonbonded pdb=" H3 MET H 1 " pdb=" O VAL H 17 " model vdw 1.543 1.850 nonbonded pdb=" O ASP E 21 " pdb=" HG1 THR E 55 " model vdw 1.549 1.850 nonbonded pdb=" O ILE H 36 " pdb="HE22 GLN H 41 " model vdw 1.609 1.850 nonbonded pdb=" O THR E 14 " pdb=" HZ1 LYS E 33 " model vdw 1.616 1.850 ... (remaining 79851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name \ HH22)))) selection = (chain 'H' and resid 1 through 72) } 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.030 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.090 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:7.460 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.025 2790 Z= 0.183 Angle : 0.555 4.394 3774 Z= 0.303 Chirality : 0.039 0.140 441 Planarity : 0.004 0.029 490 Dihedral : 13.883 79.531 1076 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.65 % Allowed : 2.27 % Favored : 97.09 % 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: -2.12 (0.43), residues: 336 helix: -1.92 (0.34), residues: 172 sheet: -0.85 (0.77), residues: 51 loop : -0.35 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 42 TYR 0.006 0.001 TYR A 13 PHE 0.011 0.001 PHE A 107 TRP 0.004 0.001 TRP A 75 HIS 0.004 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2790 Z= 0.227 Angle : 0.500 4.353 3774 Z= 0.267 Chirality : 0.051 0.180 441 Planarity : 0.003 0.023 490 Dihedral : 12.675 80.207 1076 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.46 % Favored : 95.24 % Rotamer: Outliers : 0.97 % Allowed : 2.59 % Favored : 96.44 % 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: -2.77 (0.40), residues: 336 helix: -1.91 (0.33), residues: 172 sheet: -1.65 (0.75), residues: 52 loop : -1.36 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 132 TYR 0.004 0.001 TYR A 13 PHE 0.011 0.001 PHE A 107 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2790 Z= 0.339 Angle : 0.521 4.567 3774 Z= 0.283 Chirality : 0.053 0.173 441 Planarity : 0.003 0.029 490 Dihedral : 12.377 82.890 1076 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.97 % Allowed : 3.24 % Favored : 95.79 % 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: -3.73 (0.38), residues: 336 helix: -2.23 (0.32), residues: 170 sheet: -2.23 (0.65), residues: 52 loop : -2.62 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.005 0.001 TYR A 13 PHE 0.014 0.001 PHE A 107 TRP 0.004 0.001 TRP A 71 HIS 0.005 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2790 Z= 0.261 Angle : 0.483 4.227 3774 Z= 0.260 Chirality : 0.051 0.171 441 Planarity : 0.003 0.021 490 Dihedral : 12.054 88.192 1076 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.97 % Allowed : 3.56 % Favored : 95.47 % 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: -3.65 (0.38), residues: 336 helix: -2.09 (0.33), residues: 170 sheet: -2.43 (0.64), residues: 52 loop : -2.58 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.005 0.001 TYR A 13 PHE 0.012 0.001 PHE A 107 TRP 0.003 0.001 TRP A 71 HIS 0.004 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 overall best weight: 12.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2790 Z= 0.371 Angle : 0.534 4.502 3774 Z= 0.292 Chirality : 0.053 0.181 441 Planarity : 0.003 0.029 490 Dihedral : 12.187 86.946 1076 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.52 % Favored : 89.29 % Rotamer: Outliers : 1.29 % Allowed : 4.21 % Favored : 94.50 % 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: -4.22 (0.35), residues: 336 helix: -2.39 (0.31), residues: 171 sheet: -2.60 (0.61), residues: 52 loop : -3.21 (0.43), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.004 0.001 TYR A 13 PHE 0.013 0.002 PHE A 107 TRP 0.004 0.001 TRP A 71 HIS 0.005 0.001 HIS A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2790 Z= 0.283 Angle : 0.483 4.302 3774 Z= 0.260 Chirality : 0.051 0.177 441 Planarity : 0.003 0.024 490 Dihedral : 11.821 82.868 1076 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.74 % Favored : 91.37 % Rotamer: Outliers : 1.29 % Allowed : 4.53 % Favored : 94.17 % 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: -3.66 (0.38), residues: 336 helix: -2.01 (0.33), residues: 170 sheet: -2.57 (0.62), residues: 50 loop : -2.71 (0.47), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.006 0.001 TYR A 13 PHE 0.012 0.001 PHE A 107 TRP 0.003 0.001 TRP A 75 HIS 0.004 0.001 HIS A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 191.43 seconds wall clock time: 3 minutes 51.41 seconds (231.41 seconds total)