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/7lkh_23408.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.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=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7lkh_23408.map" } resolution = 3.5 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= 0.002 sd= 0.021 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 2645 2.51 5 N 715 2.21 5 O 788 1.98 5 H 4080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 8236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4686 Inner-chain residues flagged as termini: ['pdbres="VAL A 72 "', 'pdbres="ARG A 81 "', 'pdbres="GLU A 278 "', 'pdbres="THR A 637 "'] Classifications: {'peptide': 286} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1865 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1685 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 2.41, per 1000 atoms: 0.29 Number of scatterers: 8236 At special positions: 0 Unit cell: (71.28, 100.44, 84.24, 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 788 8.00 N 715 7.00 C 2645 6.00 H 4080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 3.61 Conformation dependent library (CDL) restraints added in 546.5 milliseconds Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 20.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.618A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 191 through 198 removed outlier: 5.206A pdb=" N HIS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 656 through 666 removed outlier: 4.479A pdb=" N TRP A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Proline residue: A 660 - end of helix Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 61 through 64 Processing sheet with id= B, first strand: chain 'A' and resid 232 through 240 removed outlier: 6.140A pdb=" N ILE A 681 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS A 99 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 683 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 101 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 685 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.554A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= F, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.271A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 85 through 90 108 hydrogen bonds defined for protein. 267 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: 3.18 Time building geometry restraints manager: 3.49 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: 4079 1.14 - 1.31: 676 1.31 - 1.48: 1790 1.48 - 1.64: 1787 1.64 - 1.81: 9 Bond restraints: 8341 Sorted by residual: bond pdb=" N SER A 661 " pdb=" H SER A 661 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" N LEU H 45 " pdb=" H LEU H 45 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" N ASN A 224 " pdb=" H ASN A 224 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N GLN H 39 " pdb=" H GLN H 39 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" N TYR L 50 " pdb=" H TYR L 50 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 8336 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.70: 670 107.70 - 114.29: 9525 114.29 - 120.88: 2770 120.88 - 127.48: 2017 127.48 - 134.07: 57 Bond angle restraints: 15039 Sorted by residual: angle pdb=" N SER L 52 " pdb=" CA SER L 52 " pdb=" CB SER L 52 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 angle pdb=" CA SER A 117 " pdb=" C SER A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 120.81 118.47 2.34 8.60e-01 1.35e+00 7.42e+00 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.91e+00 angle pdb=" N SER A 117 " pdb=" CA SER A 117 " pdb=" C SER A 117 " ideal model delta sigma weight residual 112.35 109.62 2.73 1.34e+00 5.57e-01 4.14e+00 angle pdb=" N PRO A 155 " pdb=" CA PRO A 155 " pdb=" C PRO A 155 " ideal model delta sigma weight residual 113.47 110.58 2.89 1.43e+00 4.89e-01 4.09e+00 ... (remaining 15034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 2665 16.26 - 32.52: 217 32.52 - 48.77: 68 48.77 - 65.03: 28 65.03 - 81.29: 8 Dihedral angle restraints: 2986 sinusoidal: 2137 harmonic: 849 Sorted by residual: dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 381 0.029 - 0.057: 175 0.057 - 0.086: 32 0.086 - 0.114: 38 0.114 - 0.143: 12 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 635 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 155 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 66 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 118 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.018 5.00e-02 4.00e+02 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 389 2.11 - 2.73: 13130 2.73 - 3.35: 22266 3.35 - 3.98: 30686 3.98 - 4.60: 45254 Nonbonded interactions: 111725 Sorted by model distance: nonbonded pdb="HD22 ASN L 34 " pdb=" O TYR L 49 " model vdw 1.483 1.850 nonbonded pdb=" O SER A 117 " pdb=" HG SER A 120 " model vdw 1.538 1.850 nonbonded pdb=" O GLY A 87 " pdb=" HH TYR A 674 " model vdw 1.572 1.850 nonbonded pdb=" OD2 ASP A 188 " pdb=" HG1 THR A 194 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLN H 5 " pdb=" H GLN H 5 " model vdw 1.620 1.850 ... (remaining 111720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 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: 0.020 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: 0.090 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:10.950 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.055 4261 Z= 0.157 Angle : 0.554 5.275 5799 Z= 0.303 Chirality : 0.042 0.143 638 Planarity : 0.004 0.052 746 Dihedral : 12.270 81.289 1562 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.13 % Favored : 93.48 % Rotamer: Outliers : 0.43 % Allowed : 1.74 % Favored : 97.83 % 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 (0.36), residues: 506 helix: -0.64 (0.55), residues: 73 sheet: -0.68 (0.38), residues: 161 loop : -1.20 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 652 TYR 0.015 0.001 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP A 84 HIS 0.003 0.001 HIS H 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4261 Z= 0.323 Angle : 0.590 5.607 5799 Z= 0.301 Chirality : 0.067 0.337 638 Planarity : 0.004 0.040 746 Dihedral : 11.830 79.030 1562 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.29 % Favored : 89.92 % Rotamer: Outliers : 0.87 % Allowed : 1.96 % Favored : 97.17 % 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: -3.39 (0.32), residues: 506 helix: -2.51 (0.42), residues: 73 sheet: -1.68 (0.36), residues: 168 loop : -2.57 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 246 TYR 0.018 0.002 TYR L 49 PHE 0.010 0.001 PHE A 247 TRP 0.012 0.002 TRP A 84 HIS 0.002 0.001 HIS A 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 4261 Z= 0.453 Angle : 0.678 5.660 5799 Z= 0.355 Chirality : 0.069 0.350 638 Planarity : 0.006 0.050 746 Dihedral : 13.076 87.645 1562 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 2.57 % Allowed : 14.43 % Favored : 83.00 % Rotamer: Outliers : 1.96 % Allowed : 4.78 % Favored : 93.26 % 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: -4.82 (0.30), residues: 506 helix: -2.90 (0.49), residues: 71 sheet: -2.44 (0.35), residues: 172 loop : -3.91 (0.30), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 50 TYR 0.018 0.002 TYR L 49 PHE 0.012 0.002 PHE A 97 TRP 0.015 0.002 TRP A 84 HIS 0.003 0.001 HIS A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4261 Z= 0.386 Angle : 0.607 6.011 5799 Z= 0.313 Chirality : 0.067 0.305 638 Planarity : 0.004 0.035 746 Dihedral : 12.566 87.437 1562 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 3.36 % Allowed : 13.64 % Favored : 83.00 % Rotamer: Outliers : 2.83 % Allowed : 4.13 % Favored : 93.04 % 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: -4.65 (0.31), residues: 506 helix: -2.77 (0.46), residues: 70 sheet: -2.49 (0.35), residues: 172 loop : -3.66 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 50 TYR 0.021 0.002 TYR L 49 PHE 0.009 0.002 PHE A 97 TRP 0.016 0.002 TRP A 84 HIS 0.002 0.001 HIS H 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4261 Z= 0.459 Angle : 0.668 5.733 5799 Z= 0.347 Chirality : 0.070 0.317 638 Planarity : 0.005 0.047 746 Dihedral : 13.206 82.264 1562 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 4.35 % Allowed : 18.58 % Favored : 77.08 % Rotamer: Outliers : 3.26 % Allowed : 7.39 % Favored : 89.35 % 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: -4.92 (0.32), residues: 506 helix: -2.93 (0.47), residues: 70 sheet: -2.57 (0.35), residues: 174 loop : -3.95 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 50 TYR 0.024 0.002 TYR L 49 PHE 0.009 0.002 PHE A 97 TRP 0.016 0.002 TRP A 84 HIS 0.002 0.001 HIS A 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4261 Z= 0.355 Angle : 0.592 6.033 5799 Z= 0.305 Chirality : 0.066 0.275 638 Planarity : 0.004 0.038 746 Dihedral : 12.730 78.648 1562 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 4.35 % Allowed : 15.81 % Favored : 79.84 % Rotamer: Outliers : 3.04 % Allowed : 6.96 % Favored : 90.00 % 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: -4.85 (0.31), residues: 506 helix: -2.74 (0.48), residues: 70 sheet: -2.63 (0.34), residues: 172 loop : -3.85 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 30 TYR 0.020 0.002 TYR L 49 PHE 0.006 0.001 PHE A 123 TRP 0.013 0.002 TRP A 84 HIS 0.003 0.001 HIS H 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 258.98 seconds wall clock time: 5 minutes 4.83 seconds (304.83 seconds total)