Starting phenix.real_space_refine on Wed Feb 12 06:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5j_37294/02_2025/8w5j_37294.cif" } resolution = 4.4 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= 0.002 sd= 0.023 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 1 5.49 5 S 22 5.16 5 C 4718 2.51 5 N 1225 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7356 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Time building chain proxies: 6.20, per 1000 atoms: 0.84 Number of scatterers: 7356 At special positions: 0 Unit cell: (94.16, 104.86, 138.03, 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 22 16.00 P 1 15.00 O 1390 8.00 N 1225 7.00 C 4718 6.00 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 - 3.00 Amino acid : True - 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: 1.60 Conformation dependent library (CDL) restraints added in 986.4 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 37.2% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.671A pdb=" N GLN A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'E' and resid 20 through 44 removed outlier: 3.809A pdb=" N ASN E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 29 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.953A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 66 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.575A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 Processing helix chain 'L' and resid 51 through 58 removed outlier: 4.019A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.558A pdb=" N ALA M 28 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 49 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.930A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 269 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 263 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 302 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 313 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 317 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 357 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 84 through 93 removed outlier: 7.274A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 164 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 196 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU I 209 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 255 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 268 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 337 " --> pdb=" O GLN I 358 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1500 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: 2.15 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1306 1.33 - 1.45: 1978 1.45 - 1.57: 4192 1.57 - 1.69: 3 1.69 - 1.81: 36 Bond restraints: 7515 Sorted by residual: bond pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.33e-02 5.65e+03 1.40e+00 bond pdb=" CB ASP I 134 " pdb=" CG ASP I 134 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" CA VAL E 60 " pdb=" CB VAL E 60 " ideal model delta sigma weight residual 1.540 1.569 -0.029 2.70e-02 1.37e+03 1.17e+00 bond pdb=" CA VAL M 60 " pdb=" CB VAL M 60 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.08e+00 bond pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 7510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9929 1.59 - 3.19: 205 3.19 - 4.78: 40 4.78 - 6.38: 12 6.38 - 7.97: 10 Bond angle restraints: 10196 Sorted by residual: angle pdb=" CA PRO I 185 " pdb=" N PRO I 185 " pdb=" CD PRO I 185 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 124.82 130.42 -5.60 1.78e+00 3.16e-01 9.90e+00 angle pdb=" C ASN I 133 " pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 125.66 130.23 -4.57 1.85e+00 2.92e-01 6.11e+00 angle pdb=" CA LEU D 57 " pdb=" CB LEU D 57 " pdb=" CG LEU D 57 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" C SER E 59 " pdb=" N VAL E 60 " pdb=" CA VAL E 60 " ideal model delta sigma weight residual 121.70 125.78 -4.08 1.80e+00 3.09e-01 5.13e+00 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4069 17.28 - 34.56: 307 34.56 - 51.84: 43 51.84 - 69.12: 11 69.12 - 86.40: 2 Dihedral angle restraints: 4432 sinusoidal: 1714 harmonic: 2718 Sorted by residual: dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 701 0.029 - 0.058: 314 0.058 - 0.087: 85 0.087 - 0.116: 50 0.116 - 0.145: 7 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CA ILE I 353 " pdb=" N ILE I 353 " pdb=" C ILE I 353 " pdb=" CB ILE I 353 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE I 344 " pdb=" N ILE I 344 " pdb=" C ILE I 344 " pdb=" CB ILE I 344 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1154 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 184 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO I 185 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO I 185 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO I 185 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 207 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 33 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO E 34 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " 0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 302 2.72 - 3.26: 7779 3.26 - 3.81: 12230 3.81 - 4.35: 13958 4.35 - 4.90: 24143 Nonbonded interactions: 58412 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.191 3.040 nonbonded pdb=" OG SER I 151 " pdb=" OE1 GLN I 169 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 62 " pdb=" OD1 ASN A 65 " model vdw 2.231 3.040 ... (remaining 58407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'I' and resid 49 through 373) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } 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 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: 2.410 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.130 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.002 0.036 7515 Z= 0.154 Angle : 0.631 7.970 10196 Z= 0.310 Chirality : 0.039 0.145 1157 Planarity : 0.005 0.109 1298 Dihedral : 12.495 86.405 2672 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.07 (0.29), residues: 918 helix: 2.12 (0.28), residues: 324 sheet: 0.18 (0.27), residues: 378 loop : -0.30 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.016 0.001 PHE I 340 TYR 0.018 0.001 TYR I 314 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: D 54 MET cc_start: 0.8156 (ptt) cc_final: 0.7902 (ptt) REVERT: I 352 LYS cc_start: 0.9468 (mttp) cc_final: 0.9231 (mmtm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1422 time to fit residues: 16.1680 Evaluate side-chains 56 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.044646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036607 restraints weight = 74312.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037582 restraints weight = 45785.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038311 restraints weight = 32632.642| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7515 Z= 0.247 Angle : 0.647 8.806 10196 Z= 0.340 Chirality : 0.042 0.200 1157 Planarity : 0.005 0.073 1298 Dihedral : 6.948 77.335 1000 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.08 (0.29), residues: 918 helix: 2.09 (0.28), residues: 328 sheet: 0.04 (0.25), residues: 400 loop : 0.08 (0.55), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.007 0.001 HIS A 346 PHE 0.013 0.001 PHE I 116 TYR 0.016 0.002 TYR I 143 ARG 0.002 0.000 ARG I 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1339 time to fit residues: 14.7638 Evaluate side-chains 52 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN M 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.044150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036063 restraints weight = 75053.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.037042 restraints weight = 46050.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037763 restraints weight = 32710.998| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7515 Z= 0.258 Angle : 0.633 10.949 10196 Z= 0.327 Chirality : 0.040 0.171 1157 Planarity : 0.005 0.058 1298 Dihedral : 6.920 74.221 1000 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.28), residues: 918 helix: 1.94 (0.27), residues: 328 sheet: -0.02 (0.26), residues: 370 loop : -0.33 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.006 0.001 HIS A 346 PHE 0.014 0.001 PHE A 359 TYR 0.016 0.002 TYR I 314 ARG 0.002 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8783 (m-80) cc_final: 0.8329 (m-10) REVERT: I 259 LEU cc_start: 0.9287 (tp) cc_final: 0.9080 (tp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1277 time to fit residues: 14.1528 Evaluate side-chains 51 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.0020 chunk 81 optimal weight: 1.9990 chunk 46 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 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN I 99 GLN I 133 ASN I 248 GLN I 266 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036816 restraints weight = 71908.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037859 restraints weight = 43411.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.038582 restraints weight = 30129.175| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7515 Z= 0.151 Angle : 0.620 7.717 10196 Z= 0.307 Chirality : 0.042 0.179 1157 Planarity : 0.004 0.055 1298 Dihedral : 6.719 72.100 1000 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.01 (0.29), residues: 918 helix: 2.16 (0.28), residues: 328 sheet: -0.11 (0.25), residues: 400 loop : 0.08 (0.55), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.013 0.001 PHE I 359 TYR 0.012 0.001 TYR I 314 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8628 (m-80) cc_final: 0.8263 (m-10) REVERT: A 303 ILE cc_start: 0.9372 (pt) cc_final: 0.9113 (pt) REVERT: A 317 THR cc_start: 0.8554 (p) cc_final: 0.8344 (t) REVERT: I 259 LEU cc_start: 0.9208 (tp) cc_final: 0.8976 (tp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1379 time to fit residues: 16.0187 Evaluate side-chains 56 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 43 optimal weight: 0.0270 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036399 restraints weight = 73130.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037463 restraints weight = 44063.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038171 restraints weight = 30765.600| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7515 Z= 0.175 Angle : 0.605 8.571 10196 Z= 0.303 Chirality : 0.041 0.167 1157 Planarity : 0.004 0.054 1298 Dihedral : 6.635 71.679 1000 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.13 % Allowed : 2.14 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.01 (0.29), residues: 918 helix: 2.17 (0.28), residues: 328 sheet: -0.10 (0.25), residues: 406 loop : 0.03 (0.57), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.012 0.001 PHE A 359 TYR 0.011 0.001 TYR D 33 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8805 (m-80) cc_final: 0.8422 (m-10) REVERT: A 303 ILE cc_start: 0.9310 (pt) cc_final: 0.9028 (pt) REVERT: I 259 LEU cc_start: 0.9325 (tp) cc_final: 0.9097 (tp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1329 time to fit residues: 14.7033 Evaluate side-chains 54 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.0570 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.044171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036120 restraints weight = 73478.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037133 restraints weight = 44577.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037869 restraints weight = 31204.324| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7515 Z= 0.202 Angle : 0.613 10.397 10196 Z= 0.308 Chirality : 0.041 0.162 1157 Planarity : 0.004 0.058 1298 Dihedral : 6.602 70.805 1000 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 918 helix: 2.16 (0.27), residues: 328 sheet: -0.15 (0.25), residues: 406 loop : -0.03 (0.56), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.005 0.001 HIS A 346 PHE 0.014 0.001 PHE A 359 TYR 0.012 0.001 TYR D 33 ARG 0.002 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8897 (m-80) cc_final: 0.8521 (m-10) REVERT: I 259 LEU cc_start: 0.9375 (tp) cc_final: 0.9150 (tp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1322 time to fit residues: 14.4754 Evaluate side-chains 51 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN I 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.043095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.035191 restraints weight = 75139.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036168 restraints weight = 45382.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036872 restraints weight = 31766.272| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7515 Z= 0.288 Angle : 0.651 12.772 10196 Z= 0.334 Chirality : 0.041 0.148 1157 Planarity : 0.005 0.081 1298 Dihedral : 6.885 69.247 1000 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 918 helix: 1.97 (0.27), residues: 330 sheet: -0.29 (0.25), residues: 406 loop : -0.21 (0.56), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 243 HIS 0.006 0.001 HIS A 346 PHE 0.022 0.002 PHE A 359 TYR 0.014 0.002 TYR A 307 ARG 0.003 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8925 (m-80) cc_final: 0.8320 (m-80) REVERT: A 307 TYR cc_start: 0.9209 (m-80) cc_final: 0.8694 (m-80) REVERT: I 259 LEU cc_start: 0.9365 (tp) cc_final: 0.9147 (tp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1314 time to fit residues: 13.6298 Evaluate side-chains 49 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035458 restraints weight = 75014.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036484 restraints weight = 44867.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037205 restraints weight = 31063.860| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7515 Z= 0.240 Angle : 0.639 11.411 10196 Z= 0.323 Chirality : 0.041 0.157 1157 Planarity : 0.005 0.068 1298 Dihedral : 6.866 67.474 1000 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.86 % 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: 0.69 (0.29), residues: 918 helix: 2.04 (0.27), residues: 328 sheet: -0.38 (0.25), residues: 402 loop : -0.09 (0.54), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 243 HIS 0.006 0.001 HIS A 346 PHE 0.028 0.001 PHE D 42 TYR 0.013 0.002 TYR D 33 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8926 (m-80) cc_final: 0.8271 (m-80) REVERT: A 307 TYR cc_start: 0.9190 (m-80) cc_final: 0.8831 (m-80) REVERT: I 259 LEU cc_start: 0.9346 (tp) cc_final: 0.9111 (tp) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1316 time to fit residues: 13.8695 Evaluate side-chains 51 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 169 GLN I 248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.043898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035734 restraints weight = 74370.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036792 restraints weight = 44018.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037540 restraints weight = 30444.663| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7515 Z= 0.159 Angle : 0.627 8.507 10196 Z= 0.309 Chirality : 0.042 0.203 1157 Planarity : 0.005 0.062 1298 Dihedral : 6.668 68.281 1000 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.13 % Allowed : 0.76 % Favored : 99.12 % 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: 0.89 (0.29), residues: 918 helix: 2.19 (0.27), residues: 328 sheet: -0.29 (0.25), residues: 402 loop : 0.07 (0.56), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 42 HIS 0.005 0.001 HIS C 17 PHE 0.029 0.001 PHE D 42 TYR 0.012 0.001 TYR I 314 ARG 0.002 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8870 (m-80) cc_final: 0.8577 (m-10) REVERT: B 126 MET cc_start: 0.9676 (ppp) cc_final: 0.9435 (ppp) REVERT: I 164 MET cc_start: 0.9211 (pmm) cc_final: 0.9006 (pmm) REVERT: I 259 LEU cc_start: 0.9328 (tp) cc_final: 0.9017 (tp) REVERT: L 61 LEU cc_start: 0.8807 (pt) cc_final: 0.8323 (mm) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1301 time to fit residues: 15.1550 Evaluate side-chains 55 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 87 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.044476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036198 restraints weight = 73782.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037270 restraints weight = 43899.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038040 restraints weight = 30351.729| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7515 Z= 0.150 Angle : 0.625 7.737 10196 Z= 0.304 Chirality : 0.042 0.171 1157 Planarity : 0.005 0.061 1298 Dihedral : 6.466 68.843 1000 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.95 (0.29), residues: 918 helix: 2.21 (0.28), residues: 328 sheet: -0.20 (0.25), residues: 400 loop : -0.03 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 42 HIS 0.004 0.001 HIS C 43 PHE 0.028 0.001 PHE D 42 TYR 0.009 0.001 TYR A 307 ARG 0.002 0.000 ARG I 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8869 (m-80) cc_final: 0.8582 (m-10) REVERT: I 259 LEU cc_start: 0.9194 (tp) cc_final: 0.8922 (pt) REVERT: L 61 LEU cc_start: 0.8850 (pt) cc_final: 0.8328 (mm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1266 time to fit residues: 14.4265 Evaluate side-chains 58 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 0.0370 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN K 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.042359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034529 restraints weight = 76569.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.035517 restraints weight = 45392.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036193 restraints weight = 31486.292| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7515 Z= 0.365 Angle : 0.718 14.302 10196 Z= 0.369 Chirality : 0.042 0.172 1157 Planarity : 0.005 0.062 1298 Dihedral : 7.004 68.901 1000 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.53 (0.28), residues: 918 helix: 1.77 (0.27), residues: 330 sheet: -0.34 (0.25), residues: 402 loop : -0.23 (0.54), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 260 HIS 0.007 0.002 HIS A 346 PHE 0.037 0.002 PHE D 42 TYR 0.016 0.002 TYR I 114 ARG 0.004 0.001 ARG I 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.84 seconds wall clock time: 36 minutes 38.04 seconds (2198.04 seconds total)