Starting phenix.real_space_refine on Tue Feb 13 09:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_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_26054/02_2024/7tpg_26054_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpg_26054/02_2024/7tpg_26054_updated.pdb" } resolution = 3.23 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= 0.000 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 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. 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-5238/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: 3.18, per 1000 atoms: 0.67 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: 1.91 Conformation dependent library (CDL) restraints added in 943.9 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: 0.98 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: 1.24 Time building geometry restraints manager: 2.07 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 1.565 1.531 0.034 2.00e-02 2.50e+03 2.96e+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=" 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=" C3 GPP H 301 " pdb=" C5 GPP H 301 " ideal model delta sigma weight residual 1.579 1.554 0.025 2.00e-02 2.50e+03 1.50e+00 bond pdb=" CG PRO L 9 " pdb=" CD PRO L 9 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 6.95e-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 68.20 119.78 -51.58 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 85.85 120.13 -34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C2 GPP H 301 " pdb=" C3 GPP H 301 " pdb=" C4 GPP H 301 " ideal model delta sigma weight residual 152.70 120.09 32.61 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: 2602 17.88 - 35.76: 195 35.76 - 53.63: 43 53.63 - 71.51: 6 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 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: 0.790 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: 3.890 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 0.034 4888 Z= 0.172 Angle : 1.065 51.580 6650 Z= 0.454 Chirality : 0.040 0.150 763 Planarity : 0.004 0.039 826 Dihedral : 13.797 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 % Allowed : 0.40 % Favored : 99.40 % 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: 0.79 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 101 HIS 0.002 0.000 HIS H 38 PHE 0.018 0.001 PHE L 72 TYR 0.015 0.001 TYR H 115 ARG 0.007 0.000 ARG B 50 *********************** 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 : 0.539 Fit side-chains REVERT: B 34 LEU cc_start: 0.6880 (tp) cc_final: 0.6473 (tp) REVERT: B 50 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.5867 (mtm-85) REVERT: B 143 TRP cc_start: 0.8337 (m100) cc_final: 0.8084 (m-90) REVERT: B 191 ARG cc_start: 0.7140 (tmt170) cc_final: 0.6816 (tpt170) REVERT: B 216 MET cc_start: 0.5598 (mtt) cc_final: 0.5067 (mtt) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1826 time to fit residues: 23.9570 Evaluate side-chains 89 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN 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: 0.8980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.1335 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= 0.171 Angle : 0.546 7.116 6650 Z= 0.288 Chirality : 0.041 0.140 763 Planarity : 0.005 0.034 826 Dihedral : 5.071 59.370 690 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.00 % Allowed : 8.42 % Favored : 90.58 % 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: 1.30 (0.30), residues: 310 sheet: 0.59 (0.55), residues: 92 loop : -0.86 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 101 HIS 0.002 0.001 HIS B 171 PHE 0.013 0.001 PHE B 212 TYR 0.010 0.001 TYR L 37 ARG 0.003 0.000 ARG B 50 *********************** 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 96 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.527 Fit side-chains REVERT: B 34 LEU cc_start: 0.7071 (tp) cc_final: 0.6488 (mp) REVERT: B 50 ARG cc_start: 0.6547 (mtm-85) cc_final: 0.6290 (mtm-85) REVERT: B 191 ARG cc_start: 0.7177 (tmt170) cc_final: 0.6731 (tpt170) REVERT: B 216 MET cc_start: 0.5288 (mtt) cc_final: 0.5018 (mtt) REVERT: H 86 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7857 (mtp) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.1896 time to fit residues: 22.2174 Evaluate side-chains 87 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 86 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 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: 0.7680 moved from start: 0.1775 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= 0.192 Angle : 0.524 6.687 6650 Z= 0.276 Chirality : 0.040 0.140 763 Planarity : 0.005 0.033 826 Dihedral : 4.961 55.978 688 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.20 % Allowed : 11.22 % Favored : 87.58 % 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: 0.43 (0.34), residues: 620 helix: 1.17 (0.30), residues: 307 sheet: 0.52 (0.56), residues: 92 loop : -1.03 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 101 HIS 0.004 0.001 HIS B 171 PHE 0.009 0.001 PHE L 72 TYR 0.009 0.001 TYR L 37 ARG 0.002 0.000 ARG B 208 *********************** 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 92 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.574 Fit side-chains REVERT: B 79 TYR cc_start: 0.8122 (t80) cc_final: 0.7788 (t80) REVERT: B 191 ARG cc_start: 0.7251 (tmt170) cc_final: 0.6759 (tpt170) REVERT: H 9 GLU cc_start: 0.8221 (pm20) cc_final: 0.8018 (pm20) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.2034 time to fit residues: 22.2022 Evaluate side-chains 85 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2483 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= 0.219 Angle : 0.537 5.854 6650 Z= 0.284 Chirality : 0.042 0.143 763 Planarity : 0.004 0.032 826 Dihedral : 5.087 55.023 688 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.20 % Allowed : 15.23 % Favored : 83.57 % 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: 0.34 (0.35), residues: 620 helix: 0.91 (0.30), residues: 316 sheet: 0.59 (0.56), residues: 92 loop : -0.90 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 101 HIS 0.005 0.001 HIS B 171 PHE 0.012 0.001 PHE B 212 TYR 0.011 0.001 TYR H 53 ARG 0.006 0.001 ARG B 50 *********************** 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 90 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.484 Fit side-chains REVERT: B 89 ASN cc_start: 0.8660 (m-40) cc_final: 0.8414 (m-40) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.1915 time to fit residues: 20.5817 Evaluate side-chains 78 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4888 Z= 0.298 Angle : 0.575 6.097 6650 Z= 0.307 Chirality : 0.044 0.165 763 Planarity : 0.005 0.029 826 Dihedral : 5.260 50.494 688 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.20 % Allowed : 16.63 % Favored : 81.16 % 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: 0.13 (0.34), residues: 620 helix: 0.84 (0.30), residues: 311 sheet: 0.50 (0.55), residues: 92 loop : -1.13 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 101 HIS 0.006 0.001 HIS B 171 PHE 0.013 0.001 PHE L 72 TYR 0.011 0.002 TYR L 50 ARG 0.004 0.000 ARG L 67 *********************** 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 87 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.545 Fit side-chains REVERT: B 381 MET cc_start: 0.8384 (mmm) cc_final: 0.8095 (mmt) REVERT: L 25 ARG cc_start: 0.6743 (mmm160) cc_final: 0.6361 (mmm160) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.1920 time to fit residues: 19.8828 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7733 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 : 0.002 0.034 4888 Z= 0.158 Angle : 0.506 8.229 6650 Z= 0.265 Chirality : 0.040 0.155 763 Planarity : 0.004 0.028 826 Dihedral : 5.035 52.417 688 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 18.24 % Favored : 79.96 % 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 (0.35), residues: 620 helix: 1.09 (0.30), residues: 308 sheet: 0.60 (0.56), residues: 92 loop : -1.04 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 101 HIS 0.002 0.000 HIS H 38 PHE 0.009 0.001 PHE L 72 TYR 0.007 0.001 TYR H 98 ARG 0.004 0.000 ARG B 208 *********************** 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 87 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.555 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 0.1875 time to fit residues: 20.1780 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7735 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4888 Z= 0.161 Angle : 0.505 7.477 6650 Z= 0.262 Chirality : 0.040 0.161 763 Planarity : 0.004 0.028 826 Dihedral : 4.976 53.238 688 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.80 % Allowed : 17.43 % Favored : 80.76 % 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: 0.46 (0.35), residues: 620 helix: 1.18 (0.30), residues: 308 sheet: 0.59 (0.56), residues: 92 loop : -1.03 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 PHE 0.024 0.001 PHE B 212 TYR 0.010 0.001 TYR H 53 ARG 0.003 0.000 ARG B 208 *********************** 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: 9 poor density : 80 time to evaluate : 0.575 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1943 time to fit residues: 20.7877 Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7736 moved from start: 0.3118 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= 0.174 Angle : 0.518 7.015 6650 Z= 0.268 Chirality : 0.040 0.160 763 Planarity : 0.004 0.028 826 Dihedral : 4.981 53.928 688 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.60 % Allowed : 18.24 % Favored : 80.16 % 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: 0.45 (0.34), residues: 620 helix: 1.20 (0.30), residues: 308 sheet: 0.60 (0.56), residues: 92 loop : -1.10 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 PHE 0.017 0.001 PHE B 212 TYR 0.008 0.001 TYR H 98 ARG 0.003 0.000 ARG B 208 *********************** 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 84 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.625 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.2045 time to fit residues: 20.2257 Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7766 moved from start: 0.3217 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= 0.216 Angle : 0.530 7.271 6650 Z= 0.277 Chirality : 0.041 0.164 763 Planarity : 0.004 0.027 826 Dihedral : 5.046 55.283 688 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.80 % Allowed : 17.64 % Favored : 80.56 % 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: 0.42 (0.34), residues: 620 helix: 1.21 (0.30), residues: 308 sheet: 0.58 (0.55), residues: 92 loop : -1.17 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 101 HIS 0.004 0.001 HIS B 171 PHE 0.015 0.001 PHE B 212 TYR 0.009 0.001 TYR H 98 ARG 0.002 0.000 ARG B 208 *********************** 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 88 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.543 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.1964 time to fit residues: 20.1765 Evaluate side-chains 86 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 13 optimal weight: 6.9990 overall best weight: 0.5954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7729 moved from start: 0.3255 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= 0.160 Angle : 0.499 7.321 6650 Z= 0.262 Chirality : 0.040 0.162 763 Planarity : 0.004 0.027 826 Dihedral : 4.953 56.156 688 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.60 % Allowed : 18.64 % Favored : 79.76 % 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: 0.52 (0.35), residues: 620 helix: 1.28 (0.30), residues: 308 sheet: 0.66 (0.56), residues: 92 loop : -1.11 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 PHE 0.016 0.001 PHE B 212 TYR 0.013 0.001 TYR H 53 ARG 0.003 0.000 ARG B 208 ********************** 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 89 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.527 Fit side-chains REVERT: B 59 MET cc_start: 0.6507 (mmm) cc_final: 0.6235 (tmm) REVERT: B 183 MET cc_start: 0.7169 (mtt) cc_final: 0.6856 (mtp) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.1931 time to fit residues: 20.4905 Evaluate side-chains 84 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.6136 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113102 restraints weight = 6089.192| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.60 r_work: 0.3172 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4888 Z= 0.160 Angle : 0.501 7.365 6650 Z= 0.262 Chirality : 0.040 0.160 763 Planarity : 0.004 0.027 826 Dihedral : 4.969 56.353 688 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.60 % Allowed : 19.04 % Favored : 79.36 % 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: 0.55 (0.35), residues: 620 helix: 1.30 (0.31), residues: 308 sheet: 0.69 (0.56), residues: 92 loop : -1.11 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS B 171 PHE 0.016 0.001 PHE B 212 TYR 0.014 0.001 TYR H 53 ARG 0.003 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1496.90 seconds wall clock time: 27 minutes 37.00 seconds (1657.00 seconds total)