Starting phenix.real_space_refine on Sun Mar 10 16:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbw_34645/03_2024/8hbw_34645_updated.pdb" } resolution = 2.57 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= 0.003 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 18 5.16 5 C 2109 2.51 5 N 548 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2179 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'ATP': 1, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 2.78, per 1000 atoms: 0.84 Number of scatterers: 3309 At special positions: 0 Unit cell: (65.052, 71.724, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 7 15.00 O 627 8.00 N 548 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 585.2 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 4 sheets defined 54.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 12 through 41 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 77 through 93 removed outlier: 4.367A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.941A pdb=" N GLY A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.644A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 203 Processing helix chain 'A' and resid 211 through 241 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 270 through 297 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.104A pdb=" N THR B 118 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 115 through 117 removed outlier: 5.956A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 97 through 100 199 hydrogen bonds defined for protein. 573 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: 0.92 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 547 1.32 - 1.44: 902 1.44 - 1.56: 1893 1.56 - 1.68: 13 1.68 - 1.81: 27 Bond restraints: 3382 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.03e+02 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.454 -0.112 1.50e-02 4.44e+03 5.57e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.10e+01 ... (remaining 3377 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.14: 91 106.14 - 113.70: 1959 113.70 - 121.26: 1739 121.26 - 128.82: 768 128.82 - 136.38: 35 Bond angle restraints: 4592 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 119.46 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.51 -7.47 1.15e+00 7.59e-01 4.24e+01 ... (remaining 4587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1792 17.12 - 34.24: 156 34.24 - 51.36: 64 51.36 - 68.49: 14 68.49 - 85.61: 6 Dihedral angle restraints: 2032 sinusoidal: 849 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU A 100 " pdb=" CG GLU A 100 " pdb=" CD GLU A 100 " pdb=" OE1 GLU A 100 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 331 0.043 - 0.086: 138 0.086 - 0.129: 33 0.129 - 0.172: 5 0.172 - 0.214: 3 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LYS A 66 " pdb=" N LYS A 66 " pdb=" C LYS A 66 " pdb=" CB LYS A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 261 " pdb=" N GLU A 261 " pdb=" C GLU A 261 " pdb=" CB GLU A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 238 " pdb=" N ARG A 238 " pdb=" C ARG A 238 " pdb=" CB ARG A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 507 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A 10 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 84 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLN A 84 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 84 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 85 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 101 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 101 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 362 2.74 - 3.28: 3214 3.28 - 3.82: 6008 3.82 - 4.36: 7229 4.36 - 4.90: 12103 Nonbonded interactions: 28916 Sorted by model distance: nonbonded pdb=" OG1 THR A 103 " pdb=" O THR A 108 " model vdw 2.199 2.440 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 247 " model vdw 2.266 2.440 nonbonded pdb=" O LYS A 292 " pdb=" OG SER A 296 " model vdw 2.276 2.440 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.320 2.440 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.323 2.440 ... (remaining 28911 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: 0.940 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: 0.000 Extract box with map and model: 4.650 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.010 0.124 3382 Z= 0.641 Angle : 1.053 17.042 4592 Z= 0.645 Chirality : 0.050 0.214 510 Planarity : 0.005 0.057 567 Dihedral : 16.265 85.607 1275 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.39), residues: 410 helix: 1.83 (0.32), residues: 221 sheet: -0.32 (0.61), residues: 60 loop : 0.59 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 173 HIS 0.003 0.001 HIS B 124 PHE 0.018 0.003 PHE A 223 TYR 0.014 0.002 TYR A 157 ARG 0.021 0.002 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.371 Fit side-chains REVERT: A 55 LYS cc_start: 0.8108 (tttp) cc_final: 0.7810 (tptp) REVERT: A 161 ARG cc_start: 0.7447 (ttt180) cc_final: 0.6715 (mtt90) REVERT: A 206 ILE cc_start: 0.6885 (mm) cc_final: 0.6564 (mp) REVERT: A 248 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8426 (ptmt) REVERT: A 293 ARG cc_start: 0.6520 (ptm-80) cc_final: 0.6132 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.4251 time to fit residues: 90.5751 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.0020 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3382 Z= 0.189 Angle : 0.511 6.818 4592 Z= 0.267 Chirality : 0.039 0.135 510 Planarity : 0.004 0.051 567 Dihedral : 13.669 85.239 569 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.48 % Allowed : 8.31 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.40), residues: 410 helix: 2.63 (0.33), residues: 221 sheet: -0.09 (0.64), residues: 54 loop : 0.71 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.008 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.388 Fit side-chains REVERT: A 55 LYS cc_start: 0.8018 (tttp) cc_final: 0.7753 (tptp) REVERT: A 117 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7606 (tt) REVERT: A 161 ARG cc_start: 0.7365 (ttt180) cc_final: 0.6594 (mtt90) REVERT: A 206 ILE cc_start: 0.6744 (mm) cc_final: 0.6491 (mp) REVERT: A 293 ARG cc_start: 0.6328 (ptm-80) cc_final: 0.6031 (tmt-80) outliers start: 5 outliers final: 0 residues processed: 63 average time/residue: 1.2575 time to fit residues: 81.4723 Evaluate side-chains 56 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3382 Z= 0.169 Angle : 0.491 7.334 4592 Z= 0.252 Chirality : 0.038 0.129 510 Planarity : 0.004 0.046 567 Dihedral : 12.269 75.782 569 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.37 % Allowed : 11.87 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.41), residues: 410 helix: 2.89 (0.34), residues: 221 sheet: -0.07 (0.64), residues: 54 loop : 0.84 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.008 0.001 PHE A 223 TYR 0.007 0.001 TYR A 157 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.389 Fit side-chains REVERT: A 55 LYS cc_start: 0.8023 (tttp) cc_final: 0.7764 (tptp) REVERT: A 68 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 161 ARG cc_start: 0.7362 (ttt180) cc_final: 0.6572 (mtt90) REVERT: A 206 ILE cc_start: 0.6551 (mm) cc_final: 0.6297 (mp) REVERT: A 293 ARG cc_start: 0.6387 (ptm-80) cc_final: 0.6064 (tmt-80) outliers start: 8 outliers final: 3 residues processed: 60 average time/residue: 1.2905 time to fit residues: 79.6390 Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 0.0030 chunk 33 optimal weight: 0.0370 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3382 Z= 0.142 Angle : 0.473 8.194 4592 Z= 0.241 Chirality : 0.038 0.124 510 Planarity : 0.004 0.044 567 Dihedral : 11.463 73.373 569 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.08 % Allowed : 12.76 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.41), residues: 410 helix: 3.06 (0.34), residues: 221 sheet: 0.05 (0.65), residues: 54 loop : 0.88 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 111 HIS 0.001 0.000 HIS A 145 PHE 0.006 0.001 PHE A 128 TYR 0.006 0.001 TYR A 157 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.359 Fit side-chains REVERT: A 55 LYS cc_start: 0.8019 (tttp) cc_final: 0.7758 (tptp) REVERT: A 161 ARG cc_start: 0.7380 (ttt180) cc_final: 0.6604 (mtt90) REVERT: A 206 ILE cc_start: 0.6393 (mm) cc_final: 0.6143 (mp) REVERT: A 293 ARG cc_start: 0.6407 (ptm-80) cc_final: 0.6085 (tmt-80) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.2334 time to fit residues: 81.1797 Evaluate side-chains 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3382 Z= 0.188 Angle : 0.504 8.155 4592 Z= 0.258 Chirality : 0.039 0.124 510 Planarity : 0.004 0.041 567 Dihedral : 11.709 72.744 569 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.56 % Allowed : 13.65 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.41), residues: 410 helix: 3.06 (0.34), residues: 221 sheet: 0.05 (0.64), residues: 54 loop : 0.89 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 PHE 0.011 0.002 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.005 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.336 Fit side-chains REVERT: A 53 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7255 (tpt-90) REVERT: A 55 LYS cc_start: 0.8025 (tttp) cc_final: 0.7757 (tptp) REVERT: A 161 ARG cc_start: 0.7385 (ttt180) cc_final: 0.6597 (mtt90) REVERT: A 206 ILE cc_start: 0.6557 (mm) cc_final: 0.6294 (mp) REVERT: A 293 ARG cc_start: 0.6486 (ptm-80) cc_final: 0.6147 (tmt-80) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 1.2203 time to fit residues: 77.9053 Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3382 Z= 0.258 Angle : 0.538 8.278 4592 Z= 0.277 Chirality : 0.041 0.128 510 Planarity : 0.004 0.039 567 Dihedral : 12.481 74.959 569 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.56 % Allowed : 14.24 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.41), residues: 410 helix: 2.92 (0.34), residues: 221 sheet: -0.08 (0.64), residues: 54 loop : 0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 280 HIS 0.002 0.001 HIS B 124 PHE 0.013 0.002 PHE A 223 TYR 0.010 0.001 TYR A 157 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.379 Fit side-chains REVERT: A 53 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7270 (tpt-90) REVERT: A 55 LYS cc_start: 0.8081 (tttp) cc_final: 0.7749 (tptp) REVERT: A 57 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8102 (t) REVERT: A 161 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6625 (mtt90) REVERT: A 206 ILE cc_start: 0.6803 (mm) cc_final: 0.6525 (mp) REVERT: A 293 ARG cc_start: 0.6504 (ptm-80) cc_final: 0.6128 (tmt-80) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 1.2833 time to fit residues: 77.9625 Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3382 Z= 0.177 Angle : 0.504 8.528 4592 Z= 0.257 Chirality : 0.039 0.129 510 Planarity : 0.004 0.038 567 Dihedral : 12.091 73.403 569 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.97 % Allowed : 15.43 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.41), residues: 410 helix: 2.99 (0.34), residues: 221 sheet: -0.06 (0.65), residues: 54 loop : 0.86 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.009 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: A 53 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7239 (tpt-90) REVERT: A 55 LYS cc_start: 0.8046 (tttp) cc_final: 0.7748 (tptp) REVERT: A 57 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 70 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6535 (mtm-85) REVERT: A 161 ARG cc_start: 0.7396 (ttt180) cc_final: 0.6614 (mtt90) REVERT: A 206 ILE cc_start: 0.6611 (mm) cc_final: 0.6340 (mp) REVERT: A 293 ARG cc_start: 0.6480 (ptm-80) cc_final: 0.6117 (tmt-80) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 1.1725 time to fit residues: 71.2968 Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3382 Z= 0.194 Angle : 0.507 8.461 4592 Z= 0.259 Chirality : 0.039 0.126 510 Planarity : 0.004 0.037 567 Dihedral : 12.043 73.083 569 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.97 % Allowed : 15.43 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.41), residues: 410 helix: 2.99 (0.34), residues: 221 sheet: -0.09 (0.64), residues: 54 loop : 0.91 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.001 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.434 Fit side-chains REVERT: A 53 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7236 (tpt-90) REVERT: A 55 LYS cc_start: 0.8066 (tttp) cc_final: 0.7767 (tptp) REVERT: A 57 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8091 (t) REVERT: A 70 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6517 (mtm-85) REVERT: A 161 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6620 (mtt90) REVERT: A 206 ILE cc_start: 0.6614 (mm) cc_final: 0.6341 (mp) REVERT: A 293 ARG cc_start: 0.6482 (ptm-80) cc_final: 0.6121 (tmt-80) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 1.2096 time to fit residues: 72.3718 Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3382 Z= 0.178 Angle : 0.500 8.690 4592 Z= 0.254 Chirality : 0.039 0.127 510 Planarity : 0.004 0.037 567 Dihedral : 11.762 71.408 569 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.56 % Allowed : 15.13 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.41), residues: 410 helix: 3.06 (0.34), residues: 221 sheet: -0.03 (0.65), residues: 54 loop : 0.96 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.001 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.339 Fit side-chains REVERT: A 53 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7223 (tpt-90) REVERT: A 55 LYS cc_start: 0.8071 (tttp) cc_final: 0.7772 (tptp) REVERT: A 161 ARG cc_start: 0.7414 (ttt180) cc_final: 0.6623 (mtt90) REVERT: A 293 ARG cc_start: 0.6459 (ptm-80) cc_final: 0.6118 (tmt-80) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 1.1781 time to fit residues: 72.8647 Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3382 Z= 0.174 Angle : 0.521 10.416 4592 Z= 0.260 Chirality : 0.039 0.150 510 Planarity : 0.004 0.037 567 Dihedral : 11.631 69.897 569 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.67 % Allowed : 16.02 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.41), residues: 410 helix: 3.11 (0.34), residues: 221 sheet: 0.06 (0.67), residues: 54 loop : 1.03 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 280 HIS 0.001 0.000 HIS A 145 PHE 0.008 0.001 PHE A 223 TYR 0.008 0.001 TYR A 157 ARG 0.006 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.374 Fit side-chains REVERT: A 53 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7214 (tpt-90) REVERT: A 55 LYS cc_start: 0.8072 (tttp) cc_final: 0.7771 (tptp) REVERT: A 161 ARG cc_start: 0.7409 (ttt180) cc_final: 0.6620 (mtt90) REVERT: A 207 LEU cc_start: 0.6414 (mp) cc_final: 0.6090 (mm) REVERT: A 293 ARG cc_start: 0.6468 (ptm-80) cc_final: 0.6133 (tmt-80) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 1.2767 time to fit residues: 77.4307 Evaluate side-chains 62 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119427 restraints weight = 3568.455| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 0.95 r_work: 0.3195 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3382 Z= 0.187 Angle : 0.522 9.612 4592 Z= 0.262 Chirality : 0.039 0.150 510 Planarity : 0.004 0.037 567 Dihedral : 11.694 69.510 569 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 15.73 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.41), residues: 410 helix: 3.07 (0.34), residues: 221 sheet: 0.01 (0.66), residues: 54 loop : 1.05 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE A 285 TYR 0.008 0.001 TYR A 157 ARG 0.006 0.000 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.90 seconds wall clock time: 35 minutes 10.81 seconds (2110.81 seconds total)