Starting phenix.real_space_refine on Wed Feb 14 19:07:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/02_2024/7u8g_26383_trim_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 3 5.49 5 S 27 5.16 5 C 3292 2.51 5 N 827 2.21 5 O 895 1.98 5 H 4861 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9907 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4247 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 248} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2081 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "D" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1738 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1640 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'HEM': 2, 'NAG': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.13, per 1000 atoms: 0.52 Number of scatterers: 9907 At special positions: 0 Unit cell: (57.749, 70.907, 128.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 27 16.00 P 3 15.00 O 895 8.00 N 827 7.00 C 3292 6.00 H 4861 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 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=2, symmetry=0 Links applied NAG-ASN " NAG A 603 " - " ASN A 240 " " NAG A 604 " - " ASN A 149 " " NAG A 605 " - " ASN A 132 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 7 sheets defined 45.9% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 8 through 34 Processing helix chain 'A' and resid 40 through 66 removed outlier: 7.986A pdb=" N SER A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 174 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.773A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 241 through 244 No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.407A pdb=" N GLY A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.712A pdb=" N GLU B 12 " --> pdb=" O MET B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 54 Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.560A pdb=" N LEU B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 3.601A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 Proline residue: B 100 - end of helix removed outlier: 4.445A pdb=" N PHE B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 126 removed outlier: 4.330A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'A' and resid 229 through 231 Processing sheet with id= B, first strand: chain 'D' and resid 3 through 5 Processing sheet with id= C, first strand: chain 'D' and resid 115 through 117 removed outlier: 3.520A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.664A pdb=" N SER D 110 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR D 99 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU D 108 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= F, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.148A pdb=" N LYS E 106 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA E 13 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.048A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 660 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: 3.35 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 4853 1.08 - 1.33: 893 1.33 - 1.57: 4246 1.57 - 1.82: 43 1.82 - 2.06: 8 Bond restraints: 10043 Sorted by residual: bond pdb=" O12 POV B 201 " pdb=" P POV B 201 " ideal model delta sigma weight residual 1.657 1.463 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C31 POV B 201 " pdb=" O31 POV B 201 " ideal model delta sigma weight residual 1.327 1.421 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C31 POV A 602 " pdb=" O31 POV A 602 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C31 POV A 602 " pdb=" C32 POV A 602 " ideal model delta sigma weight residual 1.502 1.556 -0.054 2.00e-02 2.50e+03 7.39e+00 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 88.91 - 105.76: 92 105.76 - 122.61: 16565 122.61 - 139.46: 1358 139.46 - 156.31: 2 156.31 - 173.16: 4 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C34 POV A 602 " pdb=" C35 POV A 602 " pdb=" C36 POV A 602 " ideal model delta sigma weight residual 112.32 141.08 -28.76 3.00e+00 1.11e-01 9.19e+01 angle pdb=" C34 POV A 601 " pdb=" C35 POV A 601 " pdb=" C36 POV A 601 " ideal model delta sigma weight residual 112.32 140.31 -27.99 3.00e+00 1.11e-01 8.71e+01 angle pdb=" C34 POV B 201 " pdb=" C35 POV B 201 " pdb=" C36 POV B 201 " ideal model delta sigma weight residual 112.32 139.07 -26.75 3.00e+00 1.11e-01 7.95e+01 angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 100.63 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O13 POV A 602 " pdb=" P POV A 602 " pdb=" O14 POV A 602 " ideal model delta sigma weight residual 121.11 101.14 19.97 3.00e+00 1.11e-01 4.43e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4270 17.18 - 34.36: 354 34.36 - 51.55: 92 51.55 - 68.73: 41 68.73 - 85.91: 16 Dihedral angle restraints: 4773 sinusoidal: 2582 harmonic: 2191 Sorted by residual: dihedral pdb=" CA LEU A 66 " pdb=" C LEU A 66 " pdb=" N ILE A 67 " pdb=" CA ILE A 67 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C1A HEM A 607 " pdb=" C2A HEM A 607 " pdb=" CAA HEM A 607 " pdb=" CBA HEM A 607 " ideal model delta sinusoidal sigma weight residual 0.00 79.89 -79.89 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C2D HEM A 607 " pdb=" C3D HEM A 607 " pdb=" CAD HEM A 607 " pdb=" CBD HEM A 607 " ideal model delta sinusoidal sigma weight residual 180.00 104.07 75.93 2 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 778 0.164 - 0.327: 0 0.327 - 0.491: 0 0.491 - 0.654: 0 0.654 - 0.818: 1 Chirality restraints: 779 Sorted by residual: chirality pdb=" C5 NAG A 603 " pdb=" C4 NAG A 603 " pdb=" C6 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.41 -1.59 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ILE E 48 " pdb=" N ILE E 48 " pdb=" C ILE E 48 " pdb=" CB ILE E 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 776 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 276 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 7 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO E 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 199 " 0.098 9.50e-02 1.11e+02 3.28e-02 1.17e+00 pdb=" NE ARG A 199 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 199 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 199 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 199 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 199 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 199 " 0.000 2.00e-02 2.50e+03 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 647 2.20 - 2.80: 20127 2.80 - 3.40: 27232 3.40 - 4.00: 36519 4.00 - 4.60: 56565 Nonbonded interactions: 141090 Sorted by model distance: nonbonded pdb=" OD1 ASN B 11 " pdb="HH22 ARG B 67 " model vdw 1.603 1.850 nonbonded pdb=" HH TYR A 137 " pdb=" O GLU A 245 " model vdw 1.616 1.850 nonbonded pdb=" OE1 GLN D 39 " pdb="HE22 GLN E 38 " model vdw 1.619 1.850 nonbonded pdb=" O GLY E 68 " pdb=" HH TYR E 71 " model vdw 1.636 1.850 nonbonded pdb=" O ALA B 101 " pdb=" HG1 THR B 107 " model vdw 1.637 1.850 ... (remaining 141085 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: 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 individual isotropic 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: 4.900 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: 0.140 Extract box with map and model: 12.190 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 36.900 Find NCS groups from input model: 0.170 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.006 0.194 5182 Z= 0.424 Angle : 0.992 28.765 7060 Z= 0.388 Chirality : 0.049 0.818 779 Planarity : 0.004 0.049 851 Dihedral : 14.761 85.910 1862 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.36), residues: 611 helix: 2.04 (0.33), residues: 262 sheet: 0.40 (0.55), residues: 105 loop : -0.81 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.016 0.001 TYR B 121 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4530 time to fit residues: 36.1562 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5182 Z= 0.192 Angle : 0.506 10.181 7060 Z= 0.241 Chirality : 0.039 0.149 779 Planarity : 0.003 0.046 851 Dihedral : 10.899 84.115 807 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.04 (0.35), residues: 611 helix: 2.07 (0.33), residues: 263 sheet: 0.49 (0.54), residues: 105 loop : -0.75 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 270 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.012 0.001 TYR E 49 ARG 0.001 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4844 time to fit residues: 35.2974 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5182 Z= 0.190 Angle : 0.486 9.664 7060 Z= 0.231 Chirality : 0.039 0.145 779 Planarity : 0.003 0.042 851 Dihedral : 9.962 84.462 807 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.39 % Allowed : 6.09 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.16 (0.35), residues: 611 helix: 2.13 (0.33), residues: 265 sheet: 0.59 (0.54), residues: 105 loop : -0.70 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 155 TYR 0.011 0.001 TYR E 49 ARG 0.001 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.4635 time to fit residues: 33.9845 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5182 Z= 0.204 Angle : 0.483 9.873 7060 Z= 0.229 Chirality : 0.039 0.146 779 Planarity : 0.003 0.040 851 Dihedral : 9.320 83.366 807 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.59 % Allowed : 6.48 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.15 (0.35), residues: 611 helix: 2.16 (0.33), residues: 265 sheet: 0.59 (0.53), residues: 106 loop : -0.77 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR E 49 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.737 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.4722 time to fit residues: 36.8108 Evaluate side-chains 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5182 Z= 0.154 Angle : 0.461 9.317 7060 Z= 0.219 Chirality : 0.039 0.179 779 Planarity : 0.003 0.038 851 Dihedral : 8.875 82.717 807 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.59 % Allowed : 6.88 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.25 (0.35), residues: 611 helix: 2.23 (0.33), residues: 265 sheet: 0.65 (0.53), residues: 106 loop : -0.69 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE A 155 TYR 0.008 0.001 TYR E 49 ARG 0.003 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.4910 time to fit residues: 39.8078 Evaluate side-chains 63 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5182 Z= 0.342 Angle : 0.549 11.581 7060 Z= 0.263 Chirality : 0.040 0.145 779 Planarity : 0.004 0.039 851 Dihedral : 9.298 85.785 807 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.38 % Allowed : 7.47 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.94 (0.35), residues: 611 helix: 1.97 (0.33), residues: 265 sheet: 0.52 (0.54), residues: 105 loop : -0.87 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 106 HIS 0.006 0.002 HIS A 115 PHE 0.013 0.001 PHE A 212 TYR 0.019 0.002 TYR E 49 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8081 (mmt) cc_final: 0.7552 (mmt) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.4813 time to fit residues: 37.0904 Evaluate side-chains 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5182 Z= 0.254 Angle : 0.504 9.899 7060 Z= 0.242 Chirality : 0.040 0.147 779 Planarity : 0.003 0.039 851 Dihedral : 8.832 82.678 807 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 8.06 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.90 (0.35), residues: 611 helix: 1.93 (0.33), residues: 265 sheet: 0.47 (0.54), residues: 105 loop : -0.85 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 212 TYR 0.013 0.001 TYR E 49 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8063 (mmt) cc_final: 0.7528 (mmt) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.4626 time to fit residues: 32.9632 Evaluate side-chains 59 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5182 Z= 0.170 Angle : 0.472 10.069 7060 Z= 0.224 Chirality : 0.039 0.148 779 Planarity : 0.003 0.039 851 Dihedral : 8.420 81.118 807 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 8.45 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.35), residues: 611 helix: 2.16 (0.33), residues: 263 sheet: 0.52 (0.54), residues: 105 loop : -0.81 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE A 155 TYR 0.008 0.001 TYR A 29 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8041 (mmt) cc_final: 0.7500 (mmt) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.4914 time to fit residues: 37.0431 Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5182 Z= 0.177 Angle : 0.472 9.764 7060 Z= 0.223 Chirality : 0.039 0.147 779 Planarity : 0.003 0.038 851 Dihedral : 8.194 76.948 807 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.59 % Allowed : 8.64 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.09 (0.35), residues: 611 helix: 2.19 (0.33), residues: 264 sheet: 0.47 (0.54), residues: 106 loop : -0.83 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.005 0.001 HIS A 115 PHE 0.008 0.001 PHE A 155 TYR 0.010 0.001 TYR E 49 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.8007 (mmt) cc_final: 0.7468 (mmt) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.4852 time to fit residues: 36.2593 Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5182 Z= 0.239 Angle : 0.501 10.380 7060 Z= 0.237 Chirality : 0.039 0.146 779 Planarity : 0.003 0.040 851 Dihedral : 8.159 69.881 807 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.59 % Allowed : 8.64 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.02 (0.35), residues: 611 helix: 2.13 (0.33), residues: 263 sheet: 0.45 (0.54), residues: 105 loop : -0.87 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.005 0.001 HIS A 115 PHE 0.010 0.001 PHE A 212 TYR 0.014 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.773 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.4516 time to fit residues: 34.0696 Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119650 restraints weight = 17065.657| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.51 r_work: 0.3159 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5182 Z= 0.225 Angle : 0.495 10.013 7060 Z= 0.234 Chirality : 0.039 0.146 779 Planarity : 0.003 0.038 851 Dihedral : 7.971 65.374 807 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.79 % Allowed : 8.45 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.00 (0.35), residues: 611 helix: 2.13 (0.33), residues: 263 sheet: 0.42 (0.54), residues: 105 loop : -0.88 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 106 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 212 TYR 0.012 0.001 TYR E 49 ARG 0.004 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.45 seconds wall clock time: 58 minutes 39.26 seconds (3519.26 seconds total)