Starting phenix.real_space_refine (version: dev) on Fri Jun 3 00:39:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/06_2022/7uml_26603.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.053 sd= 1.358 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 13227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5980 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2741 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 551 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 531 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 391 Classifications: {'RNA': 13} Modifications used: {'rna3p_pyr': 12, 'rna2p_pyr': 1, '3*END': 1} Link IDs: {'rna3p': 11, 'rna2p': 1} Time building chain proxies: 6.84, per 1000 atoms: 0.52 Number of scatterers: 13227 At special positions: 0 Unit cell: (143.65, 100.3, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 13 15.00 O 1302 8.00 N 1126 7.00 C 4272 6.00 H 6477 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 38.2% alpha, 13.5% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.732A pdb=" N PHE A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.636A pdb=" N LYS A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.539A pdb=" N VAL A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.075A pdb=" N THR A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.623A pdb=" N ILE A 218 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 220 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.412A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.718A pdb=" N ASN B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.755A pdb=" N LEU B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.571A pdb=" N PHE B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.733A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.593A pdb=" N LEU C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.550A pdb=" N HIS C 192 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 193 " --> pdb=" O TRP C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'D' and resid 27 through 35 removed outlier: 4.510A pdb=" N TYR D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.420A pdb=" N LEU A 40 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 213 removed outlier: 6.959A pdb=" N ILE B 211 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 143 Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.578A pdb=" N ILE D 14 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 5 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS E 349 " --> pdb=" O LYS D 6 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6470 1.03 - 1.23: 22 1.23 - 1.42: 3001 1.42 - 1.62: 3863 1.62 - 1.81: 67 Bond restraints: 13423 Sorted by residual: bond pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.46e+00 bond pdb=" N GLY C 146 " pdb=" CA GLY C 146 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.88e-01 bond pdb=" CA PHE A 182 " pdb=" CB PHE A 182 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.66e-02 3.63e+03 6.66e-01 bond pdb=" C ASN B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 1.331 1.348 -0.017 2.07e-02 2.33e+03 6.56e-01 bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.44e-01 ... (remaining 13418 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 322 106.69 - 113.51: 15450 113.51 - 120.33: 4505 120.33 - 127.15: 3839 127.15 - 133.97: 89 Bond angle restraints: 24205 Sorted by residual: angle pdb=" C SER C 224 " pdb=" N ILE C 225 " pdb=" CA ILE C 225 " ideal model delta sigma weight residual 121.97 129.52 -7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" N ILE C 225 " pdb=" CA ILE C 225 " pdb=" C ILE C 225 " ideal model delta sigma weight residual 109.34 102.84 6.50 2.08e+00 2.31e-01 9.78e+00 angle pdb=" C ASP A 85 " pdb=" N LYS A 86 " pdb=" CA LYS A 86 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C LYS B 197 " pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.37e+00 angle pdb=" N PHE B 198 " pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 110.49 115.35 -4.86 1.69e+00 3.50e-01 8.27e+00 ... (remaining 24200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 5325 34.69 - 69.38: 110 69.38 - 104.07: 6 104.07 - 138.76: 1 138.76 - 173.45: 1 Dihedral angle restraints: 5443 sinusoidal: 2551 harmonic: 2892 Sorted by residual: dihedral pdb=" CA ILE C 225 " pdb=" C ILE C 225 " pdb=" N SER C 226 " pdb=" CA SER C 226 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" O4' U R 36 " pdb=" C1' U R 36 " pdb=" N1 U R 36 " pdb=" C2 U R 36 " ideal model delta sinusoidal sigma weight residual -160.00 13.45 -173.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U R 27 " pdb=" C1' U R 27 " pdb=" N1 U R 27 " pdb=" C2 U R 27 " ideal model delta sinusoidal sigma weight residual -160.00 -26.98 -133.02 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 5440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 703 0.034 - 0.068: 223 0.068 - 0.102: 57 0.102 - 0.135: 26 0.135 - 0.169: 6 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C1' U R 36 " pdb=" O4' U R 36 " pdb=" C2' U R 36 " pdb=" N1 U R 36 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE C 225 " pdb=" N ILE C 225 " pdb=" C ILE C 225 " pdb=" CB ILE C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 68 " pdb=" N VAL B 68 " pdb=" C VAL B 68 " pdb=" CB VAL B 68 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1012 not shown) Planarity restraints: 1933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 197 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS B 197 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 197 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 128 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO C 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 160 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 161 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.026 5.00e-02 4.00e+02 ... (remaining 1930 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1020 2.21 - 2.81: 26688 2.81 - 3.41: 33005 3.41 - 4.00: 42734 4.00 - 4.60: 65211 Nonbonded interactions: 168658 Sorted by model distance: nonbonded pdb=" HE1 TRP B 190 " pdb=" O TRP B 220 " model vdw 1.616 1.850 nonbonded pdb=" HH TYR A 152 " pdb=" OP2 U R 35 " model vdw 1.618 1.850 nonbonded pdb=" H SER A 291 " pdb=" OP2 U R 31 " model vdw 1.644 1.850 nonbonded pdb=" O ARG D 7 " pdb=" H ASN D 11 " model vdw 1.659 1.850 nonbonded pdb=" OE1 GLN E 346 " pdb=" H TYR E 355 " model vdw 1.682 1.850 ... (remaining 168653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 59 through 227)) selection = (chain 'C' and resid 58 through 227) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 37 5.16 5 C 4272 2.51 5 N 1126 2.21 5 O 1302 1.98 5 H 6477 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.190 Extract box with map and model: 4.650 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 49.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6946 Z= 0.166 Angle : 0.577 7.548 9448 Z= 0.313 Chirality : 0.040 0.169 1015 Planarity : 0.005 0.051 1173 Dihedral : 15.494 173.453 2609 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.01 % Favored : 97.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.22 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.27), residues: 798 helix: -0.80 (0.30), residues: 273 sheet: -0.74 (0.49), residues: 99 loop : -2.91 (0.26), residues: 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4111 time to fit residues: 95.9389 Evaluate side-chains 131 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 6946 Z= 0.335 Angle : 0.643 7.764 9448 Z= 0.345 Chirality : 0.041 0.164 1015 Planarity : 0.006 0.069 1173 Dihedral : 12.423 171.286 1044 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.15 % Favored : 90.23 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.28), residues: 798 helix: -0.39 (0.30), residues: 284 sheet: -0.72 (0.45), residues: 119 loop : -2.96 (0.27), residues: 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 145 average time/residue: 0.3873 time to fit residues: 74.6782 Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1479 time to fit residues: 5.6170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 6946 Z= 0.244 Angle : 0.604 18.000 9448 Z= 0.311 Chirality : 0.040 0.182 1015 Planarity : 0.005 0.050 1173 Dihedral : 12.380 174.208 1044 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.64 % Favored : 91.98 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 798 helix: -0.02 (0.32), residues: 278 sheet: -0.83 (0.44), residues: 119 loop : -2.77 (0.28), residues: 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 137 average time/residue: 0.3985 time to fit residues: 72.4183 Evaluate side-chains 131 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1356 time to fit residues: 2.2200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 6946 Z= 0.302 Angle : 0.613 7.904 9448 Z= 0.326 Chirality : 0.041 0.180 1015 Planarity : 0.005 0.043 1173 Dihedral : 12.387 172.687 1044 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.65 % Favored : 88.85 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.28), residues: 798 helix: -0.08 (0.32), residues: 279 sheet: -0.86 (0.44), residues: 119 loop : -2.87 (0.27), residues: 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.4034 time to fit residues: 70.3808 Evaluate side-chains 130 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1511 time to fit residues: 3.8625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 6946 Z= 0.244 Angle : 0.618 16.161 9448 Z= 0.332 Chirality : 0.040 0.187 1015 Planarity : 0.005 0.039 1173 Dihedral : 12.345 173.847 1044 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.40 % Favored : 90.10 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 798 helix: 0.05 (0.32), residues: 279 sheet: -0.79 (0.44), residues: 119 loop : -2.79 (0.27), residues: 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.4107 time to fit residues: 72.4139 Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.152 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1705 time to fit residues: 2.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.172 6946 Z= 0.275 Angle : 0.637 23.799 9448 Z= 0.324 Chirality : 0.039 0.185 1015 Planarity : 0.005 0.058 1173 Dihedral : 12.280 173.894 1044 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.03 % Favored : 89.47 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.93 (0.29), residues: 798 helix: 0.13 (0.32), residues: 284 sheet: -0.69 (0.44), residues: 119 loop : -2.64 (0.28), residues: 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 0.3914 time to fit residues: 69.2935 Evaluate side-chains 131 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.156 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1552 time to fit residues: 3.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.188 6946 Z= 0.290 Angle : 0.621 13.924 9448 Z= 0.332 Chirality : 0.040 0.181 1015 Planarity : 0.005 0.103 1173 Dihedral : 12.293 173.122 1044 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.15 % Favored : 89.35 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.29), residues: 798 helix: 0.14 (0.32), residues: 284 sheet: -0.73 (0.44), residues: 119 loop : -2.66 (0.28), residues: 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 129 average time/residue: 0.3908 time to fit residues: 67.9823 Evaluate side-chains 128 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.113 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1805 time to fit residues: 2.5796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.0030 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.9170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.514 6946 Z= 0.546 Angle : 1.044 73.900 9448 Z= 0.457 Chirality : 0.040 0.187 1015 Planarity : 0.005 0.076 1173 Dihedral : 12.306 173.215 1044 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.40 % Favored : 89.10 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.29), residues: 798 helix: 0.15 (0.32), residues: 284 sheet: -0.74 (0.45), residues: 119 loop : -2.66 (0.28), residues: 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 126 average time/residue: 0.3743 time to fit residues: 63.5840 Evaluate side-chains 127 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.065 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1734 time to fit residues: 2.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.514 6946 Z= 0.561 Angle : 1.088 73.900 9448 Z= 0.492 Chirality : 0.040 0.187 1015 Planarity : 0.005 0.088 1173 Dihedral : 12.306 173.215 1044 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.40 % Favored : 89.10 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.29), residues: 798 helix: 0.15 (0.32), residues: 284 sheet: -0.74 (0.45), residues: 119 loop : -2.66 (0.28), residues: 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.3928 time to fit residues: 66.5788 Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.107 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2515 time to fit residues: 1.7238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.514 6946 Z= 0.561 Angle : 1.088 73.900 9448 Z= 0.492 Chirality : 0.040 0.187 1015 Planarity : 0.005 0.088 1173 Dihedral : 12.306 173.215 1044 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.40 % Favored : 89.10 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.29), residues: 798 helix: 0.15 (0.32), residues: 284 sheet: -0.74 (0.45), residues: 119 loop : -2.66 (0.28), residues: 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.3672 time to fit residues: 61.7739 Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.185 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2366 time to fit residues: 1.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164408 restraints weight = 31124.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168835 restraints weight = 14658.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171632 restraints weight = 8844.594| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4252 r_free = 0.4252 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4251 r_free = 0.4251 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.514 6946 Z= 0.561 Angle : 1.088 73.900 9448 Z= 0.492 Chirality : 0.040 0.187 1015 Planarity : 0.005 0.088 1173 Dihedral : 12.306 173.215 1044 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.40 % Favored : 89.10 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.95 (0.29), residues: 798 helix: 0.15 (0.32), residues: 284 sheet: -0.74 (0.45), residues: 119 loop : -2.66 (0.28), residues: 395 =============================================================================== Job complete usr+sys time: 3372.42 seconds wall clock time: 60 minutes 18.65 seconds (3618.65 seconds total)