Starting phenix.real_space_refine on Wed Nov 15 00:12:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/11_2023/7u8g_26383_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/11_2023/7u8g_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_26383/11_2023/7u8g_26383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/11_2023/7u8g_26383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/11_2023/7u8g_26383_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u8g_26383/11_2023/7u8g_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-1.21rc1-5144/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: 42 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: 27 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: 5.24, per 1000 atoms: 0.53 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: 8.70 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: 1.67 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: 3.41 Time building geometry restraints manager: 8.99 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: 3647 17.18 - 34.36: 298 34.36 - 51.55: 47 51.55 - 68.73: 6 68.73 - 85.91: 16 Dihedral angle restraints: 4014 sinusoidal: 1823 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 4011 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: 3.580 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: 0.150 Extract box with map and model: 12.130 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.310 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.170 ------------------------------------------------------------------------------- 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 : 14.550 85.910 1793 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 *********************** 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 : 0.790 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4597 time to fit residues: 36.9552 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0153 ------------------------------------------------------------------------------- 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: 0.2980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.0485 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= 0.201 Angle : 0.508 10.103 7060 Z= 0.243 Chirality : 0.039 0.151 779 Planarity : 0.003 0.047 851 Dihedral : 10.180 86.261 738 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: 1.03 (0.35), residues: 611 helix: 2.05 (0.33), residues: 263 sheet: 0.49 (0.54), residues: 105 loop : -0.76 (0.40), residues: 243 *********************** 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 : 0.807 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.5007 time to fit residues: 36.4809 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0231 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.0650 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= 0.202 Angle : 0.490 9.818 7060 Z= 0.233 Chirality : 0.039 0.145 779 Planarity : 0.003 0.043 851 Dihedral : 9.488 89.502 738 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.59 % Allowed : 6.09 % Favored : 93.32 % 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: 1.12 (0.35), residues: 611 helix: 2.10 (0.33), residues: 265 sheet: 0.56 (0.53), residues: 105 loop : -0.72 (0.40), residues: 241 *********************** 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 62 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.856 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.5077 time to fit residues: 37.8810 Evaluate side-chains 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1278 time to fit residues: 1.2940 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 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: 0.7980 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5182 Z= 0.260 Angle : 0.514 10.717 7060 Z= 0.245 Chirality : 0.040 0.148 779 Planarity : 0.003 0.042 851 Dihedral : 9.448 87.887 738 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.59 % Allowed : 6.68 % Favored : 92.73 % 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: 2.02 (0.33), residues: 265 sheet: 0.52 (0.53), residues: 105 loop : -0.83 (0.40), residues: 241 *********************** 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 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.815 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.4657 time to fit residues: 34.2846 Evaluate side-chains 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1723 time to fit residues: 1.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.0859 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= 0.215 Angle : 0.490 9.694 7060 Z= 0.233 Chirality : 0.039 0.147 779 Planarity : 0.003 0.040 851 Dihedral : 9.063 89.598 738 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.39 % Allowed : 8.06 % Favored : 91.55 % 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: 1.05 (0.35), residues: 611 helix: 2.07 (0.33), residues: 265 sheet: 0.51 (0.53), residues: 105 loop : -0.79 (0.40), residues: 241 *********************** 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 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.848 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.4217 time to fit residues: 30.4026 Evaluate side-chains 56 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1073 time to fit residues: 1.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5182 Z= 0.294 Angle : 0.525 10.726 7060 Z= 0.251 Chirality : 0.040 0.149 779 Planarity : 0.003 0.040 851 Dihedral : 8.763 87.044 738 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.59 % Allowed : 8.06 % Favored : 91.36 % 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: 0.88 (0.35), residues: 611 helix: 1.94 (0.33), residues: 265 sheet: 0.42 (0.54), residues: 105 loop : -0.89 (0.39), residues: 241 *********************** 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 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.770 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.4964 time to fit residues: 36.2611 Evaluate side-chains 56 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1579 time to fit residues: 1.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.1017 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= 0.179 Angle : 0.487 10.073 7060 Z= 0.231 Chirality : 0.039 0.149 779 Planarity : 0.003 0.040 851 Dihedral : 8.358 87.571 738 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.20 % Allowed : 8.25 % Favored : 91.55 % 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: 1.06 (0.35), residues: 611 helix: 2.09 (0.33), residues: 265 sheet: 0.47 (0.54), residues: 105 loop : -0.78 (0.40), residues: 241 *********************** 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 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4921 time to fit residues: 36.5465 Evaluate side-chains 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1128 time to fit residues: 1.1599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.1082 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= 0.218 Angle : 0.496 9.922 7060 Z= 0.235 Chirality : 0.040 0.190 779 Planarity : 0.003 0.039 851 Dihedral : 8.145 87.308 738 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.39 % Allowed : 8.64 % Favored : 90.96 % 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: 2.08 (0.33), residues: 264 sheet: 0.45 (0.54), residues: 105 loop : -0.85 (0.40), residues: 242 *********************** 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 59 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.750 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.4714 time to fit residues: 34.3166 Evaluate side-chains 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1417 time to fit residues: 1.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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: 0.8140 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5182 Z= 0.167 Angle : 0.479 10.079 7060 Z= 0.228 Chirality : 0.039 0.148 779 Planarity : 0.003 0.039 851 Dihedral : 7.928 87.261 738 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.20 % Allowed : 9.43 % Favored : 90.37 % 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: 1.11 (0.36), residues: 611 helix: 2.18 (0.33), residues: 263 sheet: 0.51 (0.54), residues: 105 loop : -0.79 (0.40), residues: 243 *********************** 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 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.5250 time to fit residues: 37.7513 Evaluate side-chains 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5182 Z= 0.241 Angle : 0.508 10.235 7060 Z= 0.239 Chirality : 0.040 0.147 779 Planarity : 0.003 0.038 851 Dihedral : 7.939 86.378 738 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % 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: 2.12 (0.33), residues: 263 sheet: 0.49 (0.54), residues: 105 loop : -0.84 (0.40), residues: 243 ********************** 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 57 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.764 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4911 time to fit residues: 34.6519 Evaluate side-chains 56 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119991 restraints weight = 17063.441| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.52 r_work: 0.2978 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1182 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= 0.197 Angle : 0.497 10.178 7060 Z= 0.234 Chirality : 0.039 0.147 779 Planarity : 0.003 0.039 851 Dihedral : 7.845 86.242 738 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % 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: 1.07 (0.35), residues: 611 helix: 2.14 (0.33), residues: 263 sheet: 0.49 (0.54), residues: 105 loop : -0.80 (0.40), residues: 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.88 seconds wall clock time: 58 minutes 48.70 seconds (3528.70 seconds total)