Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:50:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/11_2022/7tpg_26054_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 315": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4777 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3053 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'GPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.66 Number of scatterers: 4777 At special positions: 0 Unit cell: (76.392, 77.453, 107.161, 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 32 16.00 P 2 15.00 O 846 8.00 N 816 7.00 C 3081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 2.06 Conformation dependent library (CDL) restraints added in 727.7 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 5 sheets defined 49.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.525A pdb=" N LEU B 15 " --> pdb=" O MET B 11 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.571A pdb=" N LEU B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.794A pdb=" N LEU B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 95 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 removed outlier: 4.095A pdb=" N TRP B 114 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 115 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 133 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.668A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 208 removed outlier: 3.871A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Proline residue: B 203 - end of helix removed outlier: 4.541A pdb=" N MET B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.535A pdb=" N TYR B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.857A pdb=" N ASP B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.568A pdb=" N TRP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.628A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 315 through 352 removed outlier: 7.760A pdb=" N ILE B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix removed outlier: 3.813A pdb=" N PHE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 355 through 375 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 384 through 406 Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.755A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.998A pdb=" N TYR H 115 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 20 through 24 Processing sheet with id= E, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.976A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 630 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: 1.32 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1508 1.35 - 1.46: 1231 1.46 - 1.58: 2091 1.58 - 1.70: 3 1.70 - 1.82: 55 Bond restraints: 4888 Sorted by residual: bond pdb=" C5 GPP H 301 " pdb=" C6 GPP H 301 " ideal model delta sigma weight residual 1.566 1.531 0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" CA GLY B 353 " pdb=" C GLY B 353 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.42e+00 bond pdb=" C3 GPP H 301 " pdb=" C5 GPP H 301 " ideal model delta sigma weight residual 1.580 1.554 0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" N GLY B 353 " pdb=" CA GLY B 353 " ideal model delta sigma weight residual 1.464 1.450 0.014 1.12e-02 7.97e+03 1.59e+00 bond pdb=" C2 GPP H 301 " pdb=" C3 GPP H 301 " ideal model delta sigma weight residual 1.350 1.331 0.019 2.00e-02 2.50e+03 8.96e-01 ... (remaining 4883 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.34: 140 106.34 - 113.33: 2691 113.33 - 120.32: 1746 120.32 - 127.31: 2010 127.31 - 134.31: 63 Bond angle restraints: 6650 Sorted by residual: angle pdb=" C4 GPP H 301 " pdb=" C3 GPP H 301 " pdb=" C5 GPP H 301 " ideal model delta sigma weight residual 68.18 119.78 -51.60 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C2 GPP H 301 " pdb=" C3 GPP H 301 " pdb=" C5 GPP H 301 " ideal model delta sigma weight residual 85.86 120.13 -34.27 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C2 GPP H 301 " pdb=" C3 GPP H 301 " pdb=" C4 GPP H 301 " ideal model delta sigma weight residual 152.68 120.09 32.59 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C HIS B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 122.74 134.31 -11.57 2.44e+00 1.68e-01 2.25e+01 angle pdb=" N ARG B 211 " pdb=" CA ARG B 211 " pdb=" C ARG B 211 " ideal model delta sigma weight residual 114.64 109.04 5.60 1.52e+00 4.33e-01 1.36e+01 ... (remaining 6645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2601 17.88 - 35.76: 195 35.76 - 53.63: 43 53.63 - 71.51: 7 71.51 - 89.39: 6 Dihedral angle restraints: 2852 sinusoidal: 1065 harmonic: 1787 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 146.21 -53.21 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLN B 255 " pdb=" C GLN B 255 " pdb=" N GLY B 256 " pdb=" CA GLY B 256 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG B 254 " pdb=" C ARG B 254 " pdb=" N GLN B 255 " pdb=" CA GLN B 255 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 464 0.030 - 0.060: 210 0.060 - 0.090: 55 0.090 - 0.120: 28 0.120 - 0.150: 6 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ASP H 114 " pdb=" N ASP H 114 " pdb=" C ASP H 114 " pdb=" CB ASP H 114 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA THR B 60 " pdb=" N THR B 60 " pdb=" C THR B 60 " pdb=" CB THR B 60 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB THR B 323 " pdb=" CA THR B 323 " pdb=" OG1 THR B 323 " pdb=" CG2 THR B 323 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 760 not shown) Planarity restraints: 826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " -0.022 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP B 101 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 89 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 90 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 107 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 108 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.018 5.00e-02 4.00e+02 ... (remaining 823 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 39 2.64 - 3.21: 4424 3.21 - 3.77: 7291 3.77 - 4.34: 9803 4.34 - 4.90: 16648 Nonbonded interactions: 38205 Sorted by model distance: nonbonded pdb=" O SER B 56 " pdb=" OG1 THR B 60 " model vdw 2.078 2.440 nonbonded pdb=" OG SER H 55 " pdb=" OG SER H 60 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASP H 114 " pdb=" N TYR H 115 " model vdw 2.237 2.520 nonbonded pdb=" OD1 ASP B 166 " pdb=" NH1 ARG B 211 " model vdw 2.315 2.520 nonbonded pdb=" NH1 ARG L 62 " pdb=" OD2 ASP L 83 " model vdw 2.331 2.520 ... (remaining 38200 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 3081 2.51 5 N 816 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.650 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: 4.390 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4888 Z= 0.174 Angle : 1.065 51.600 6650 Z= 0.454 Chirality : 0.040 0.150 763 Planarity : 0.004 0.039 826 Dihedral : 13.884 89.388 1705 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.79 (0.35), residues: 620 helix: 1.46 (0.30), residues: 310 sheet: 0.49 (0.57), residues: 87 loop : -0.76 (0.42), residues: 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.533 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1832 time to fit residues: 24.1513 Evaluate side-chains 90 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0486 time to fit residues: 0.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4888 Z= 0.191 Angle : 0.554 7.112 6650 Z= 0.293 Chirality : 0.041 0.143 763 Planarity : 0.005 0.033 826 Dihedral : 5.209 57.751 688 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.64 (0.34), residues: 620 helix: 1.32 (0.30), residues: 308 sheet: 0.58 (0.55), residues: 92 loop : -0.88 (0.42), residues: 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.600 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.1710 time to fit residues: 20.5803 Evaluate side-chains 85 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0545 time to fit residues: 1.0211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 4888 Z= 0.165 Angle : 0.503 6.858 6650 Z= 0.266 Chirality : 0.040 0.141 763 Planarity : 0.004 0.034 826 Dihedral : 5.245 59.834 688 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.51 (0.34), residues: 620 helix: 1.27 (0.30), residues: 304 sheet: 0.60 (0.55), residues: 92 loop : -1.04 (0.41), residues: 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.527 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 88 average time/residue: 0.1854 time to fit residues: 20.4715 Evaluate side-chains 84 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0470 time to fit residues: 0.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 151 ASN B 251 GLN B 354 ASN H 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4888 Z= 0.225 Angle : 0.539 5.690 6650 Z= 0.286 Chirality : 0.042 0.146 763 Planarity : 0.005 0.031 826 Dihedral : 5.197 51.547 688 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.34), residues: 620 helix: 0.89 (0.30), residues: 316 sheet: 0.52 (0.57), residues: 90 loop : -1.08 (0.42), residues: 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.543 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.1945 time to fit residues: 21.5953 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0467 time to fit residues: 0.8959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4888 Z= 0.253 Angle : 0.544 6.148 6650 Z= 0.290 Chirality : 0.042 0.158 763 Planarity : 0.005 0.038 826 Dihedral : 5.155 50.281 688 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.17 (0.34), residues: 620 helix: 0.93 (0.30), residues: 311 sheet: 0.39 (0.55), residues: 90 loop : -1.13 (0.41), residues: 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.560 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.1946 time to fit residues: 20.4815 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0542 time to fit residues: 1.0134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 85 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4888 Z= 0.206 Angle : 0.528 8.110 6650 Z= 0.278 Chirality : 0.041 0.160 763 Planarity : 0.004 0.028 826 Dihedral : 5.068 51.010 688 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.23 (0.34), residues: 620 helix: 0.98 (0.30), residues: 312 sheet: 0.46 (0.56), residues: 90 loop : -1.14 (0.41), residues: 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.524 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 0.1974 time to fit residues: 20.1966 Evaluate side-chains 79 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0474 time to fit residues: 0.9027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 4888 Z= 0.156 Angle : 0.501 7.205 6650 Z= 0.264 Chirality : 0.040 0.147 763 Planarity : 0.004 0.028 826 Dihedral : 4.885 51.846 688 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.33 (0.35), residues: 620 helix: 1.02 (0.30), residues: 316 sheet: 0.54 (0.56), residues: 90 loop : -1.08 (0.42), residues: 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.550 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 89 average time/residue: 0.1972 time to fit residues: 21.8570 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 85 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4888 Z= 0.181 Angle : 0.514 7.013 6650 Z= 0.269 Chirality : 0.040 0.153 763 Planarity : 0.004 0.039 826 Dihedral : 4.899 52.543 688 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.39 (0.34), residues: 620 helix: 1.16 (0.31), residues: 310 sheet: 0.59 (0.57), residues: 90 loop : -1.16 (0.40), residues: 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.570 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 85 average time/residue: 0.2020 time to fit residues: 21.6016 Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0497 time to fit residues: 0.9308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4888 Z= 0.191 Angle : 0.529 7.212 6650 Z= 0.274 Chirality : 0.041 0.152 763 Planarity : 0.004 0.039 826 Dihedral : 4.909 53.072 688 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.38 (0.34), residues: 620 helix: 1.15 (0.30), residues: 310 sheet: 0.60 (0.57), residues: 90 loop : -1.16 (0.40), residues: 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1973 time to fit residues: 21.3478 Evaluate side-chains 81 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 85 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4888 Z= 0.175 Angle : 0.512 7.351 6650 Z= 0.267 Chirality : 0.040 0.155 763 Planarity : 0.004 0.036 826 Dihedral : 4.887 53.634 688 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.47 (0.34), residues: 620 helix: 1.24 (0.30), residues: 309 sheet: 0.61 (0.57), residues: 90 loop : -1.11 (0.41), residues: 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.535 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.1907 time to fit residues: 19.6029 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0569 time to fit residues: 0.8892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** H 6 GLN ** 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 = 0.3426 r_free = 0.3426 target = 0.125742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112855 restraints weight = 6136.685| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.55 r_work: 0.3268 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3247 rms_B_bonded: 1.45 restraints_weight: 0.1250 r_work: 0.3235 rms_B_bonded: 1.55 restraints_weight: 0.0625 r_work: 0.3222 rms_B_bonded: 1.70 restraints_weight: 0.0312 r_work: 0.3208 rms_B_bonded: 1.88 restraints_weight: 0.0156 r_work: 0.3192 rms_B_bonded: 2.11 restraints_weight: 0.0078 r_work: 0.3175 rms_B_bonded: 2.38 restraints_weight: 0.0039 r_work: 0.3155 rms_B_bonded: 2.70 restraints_weight: 0.0020 r_work: 0.3133 rms_B_bonded: 3.08 restraints_weight: 0.0010 r_work: 0.3108 rms_B_bonded: 3.52 restraints_weight: 0.0005 r_work: 0.3080 rms_B_bonded: 4.03 restraints_weight: 0.0002 r_work: 0.3048 rms_B_bonded: 4.63 restraints_weight: 0.0001 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4888 Z= 0.172 Angle : 0.509 7.346 6650 Z= 0.265 Chirality : 0.040 0.153 763 Planarity : 0.004 0.037 826 Dihedral : 4.866 54.137 688 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.49 (0.34), residues: 620 helix: 1.26 (0.30), residues: 309 sheet: 0.63 (0.57), residues: 90 loop : -1.12 (0.41), residues: 221 =============================================================================== Job complete usr+sys time: 1309.87 seconds wall clock time: 24 minutes 36.18 seconds (1476.18 seconds total)