Starting phenix.real_space_refine on Thu Jul 18 21:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p16_13157/07_2024/7p16_13157.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 23 5.16 5 C 2412 2.51 5 N 561 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2617 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 7, 'TRANS': 310} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.82, per 1000 atoms: 0.78 Number of scatterers: 3621 At special positions: 0 Unit cell: (76.818, 102.858, 70.308, 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 23 16.00 P 1 15.00 O 624 8.00 N 561 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " 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: 1.49 Conformation dependent library (CDL) restraints added in 650.1 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 68.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.587A pdb=" N PHE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 10 " --> pdb=" O CYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.482A pdb=" N THR A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.565A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.605A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 3.521A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.092A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 removed outlier: 3.723A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 198 through 227 removed outlier: 4.140A pdb=" N LYS A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.576A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.761A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.394A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 removed outlier: 3.992A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.754A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.518A pdb=" N LYS B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.684A pdb=" N THR B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 105 " --> pdb=" O TYR B 38 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 526 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 2 1.69 - 1.81: 34 Bond restraints: 3718 Sorted by residual: bond pdb=" C' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB PLC A 401 " pdb=" O3 PLC A 401 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " ideal model delta sigma weight residual 1.503 1.553 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C4 PLC A 401 " pdb=" C5 PLC A 401 " ideal model delta sigma weight residual 1.511 1.558 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" CB PLC A 401 " pdb=" C1B PLC A 401 " ideal model delta sigma weight residual 1.504 1.551 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 3713 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.96: 70 106.96 - 113.72: 2033 113.72 - 120.47: 1486 120.47 - 127.23: 1424 127.23 - 133.99: 39 Bond angle restraints: 5052 Sorted by residual: angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 109.68 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C5 PLC A 401 " pdb=" N PLC A 401 " pdb=" C7 PLC A 401 " ideal model delta sigma weight residual 106.97 119.04 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N LEU B 114 " pdb=" CA LEU B 114 " pdb=" C LEU B 114 " ideal model delta sigma weight residual 114.56 109.89 4.67 1.27e+00 6.20e-01 1.35e+01 angle pdb=" C ILE A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" O1P PLC A 401 " pdb=" P PLC A 401 " pdb=" O2P PLC A 401 " ideal model delta sigma weight residual 119.61 109.03 10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 5047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 2023 30.46 - 60.92: 89 60.92 - 91.38: 10 91.38 - 121.85: 0 121.85 - 152.31: 2 Dihedral angle restraints: 2124 sinusoidal: 827 harmonic: 1297 Sorted by residual: dihedral pdb=" C2' PLC A 401 " pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sinusoidal sigma weight residual 169.53 17.22 152.31 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C2' PLC A 401 " pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " pdb=" O' PLC A 401 " ideal model delta sinusoidal sigma weight residual -11.03 -161.60 150.57 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CA ILE A 16 " pdb=" C ILE A 16 " pdb=" N ILE A 17 " pdb=" CA ILE A 17 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 385 0.033 - 0.067: 148 0.067 - 0.100: 30 0.100 - 0.133: 8 0.133 - 0.166: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 569 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 190 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 191 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 73 " 0.130 9.50e-02 1.11e+02 5.86e-02 2.24e+00 pdb=" NE ARG B 73 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 73 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 73 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 73 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 123 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" CD GLU A 123 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 123 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 123 " 0.008 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 100 2.72 - 3.27: 3862 3.27 - 3.81: 5788 3.81 - 4.36: 6594 4.36 - 4.90: 11142 Nonbonded interactions: 27486 Sorted by model distance: nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.178 2.520 nonbonded pdb=" NZ LYS A 209 " pdb=" OG1 THR A 274 " model vdw 2.261 2.520 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 181 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLU B 12 " pdb=" N GLY B 125 " model vdw 2.347 2.520 nonbonded pdb=" O CYS B 28 " pdb=" OG1 THR B 84 " model vdw 2.357 2.440 ... (remaining 27481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.004 0.093 3718 Z= 0.282 Angle : 0.733 16.060 5052 Z= 0.340 Chirality : 0.037 0.166 572 Planarity : 0.004 0.059 604 Dihedral : 16.470 152.308 1297 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.40), residues: 436 helix: 0.55 (0.32), residues: 249 sheet: 0.04 (0.84), residues: 44 loop : -1.00 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 101 PHE 0.016 0.001 PHE A 275 TYR 0.017 0.001 TYR A 92 ARG 0.007 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.396 Fit side-chains REVERT: A 146 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8783 (tm-30) REVERT: A 279 LYS cc_start: 0.7234 (tttt) cc_final: 0.6998 (mttt) REVERT: B 42 TRP cc_start: 0.8513 (m100) cc_final: 0.7949 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1651 time to fit residues: 26.0329 Evaluate side-chains 114 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3718 Z= 0.223 Angle : 0.603 7.161 5052 Z= 0.308 Chirality : 0.040 0.135 572 Planarity : 0.004 0.053 604 Dihedral : 10.634 104.993 524 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.26 % Allowed : 7.22 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.40), residues: 436 helix: 1.10 (0.30), residues: 262 sheet: 0.46 (0.78), residues: 50 loop : -1.06 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 122 HIS 0.001 0.001 HIS A 250 PHE 0.023 0.002 PHE A 225 TYR 0.019 0.001 TYR A 208 ARG 0.004 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.393 Fit side-chains REVERT: A 250 HIS cc_start: 0.5213 (t70) cc_final: 0.4947 (t70) REVERT: A 259 MET cc_start: 0.8233 (mmp) cc_final: 0.7722 (mmp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1497 time to fit residues: 25.1169 Evaluate side-chains 120 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3718 Z= 0.207 Angle : 0.580 7.485 5052 Z= 0.292 Chirality : 0.040 0.142 572 Planarity : 0.004 0.050 604 Dihedral : 9.212 77.559 524 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.26 % Allowed : 5.15 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.40), residues: 436 helix: 1.27 (0.30), residues: 262 sheet: 0.69 (0.92), residues: 37 loop : -1.15 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.001 0.000 HIS A 250 PHE 0.016 0.001 PHE A 225 TYR 0.018 0.001 TYR A 92 ARG 0.004 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.351 Fit side-chains REVERT: A 202 LYS cc_start: 0.8446 (mttt) cc_final: 0.8185 (mttt) REVERT: A 250 HIS cc_start: 0.5364 (t70) cc_final: 0.4944 (t70) REVERT: A 259 MET cc_start: 0.8216 (mmp) cc_final: 0.7557 (mmp) REVERT: A 279 LYS cc_start: 0.7039 (tttt) cc_final: 0.6793 (tttt) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1566 time to fit residues: 26.3683 Evaluate side-chains 116 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3718 Z= 0.213 Angle : 0.587 7.490 5052 Z= 0.294 Chirality : 0.040 0.143 572 Planarity : 0.004 0.053 604 Dihedral : 8.374 63.063 524 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.41), residues: 436 helix: 1.34 (0.31), residues: 264 sheet: 0.69 (0.90), residues: 37 loop : -1.02 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 42 HIS 0.004 0.001 HIS A 56 PHE 0.014 0.001 PHE A 47 TYR 0.018 0.001 TYR A 92 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.387 Fit side-chains REVERT: B 42 TRP cc_start: 0.8528 (m100) cc_final: 0.7905 (m100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1564 time to fit residues: 25.9868 Evaluate side-chains 117 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3718 Z= 0.176 Angle : 0.583 7.482 5052 Z= 0.284 Chirality : 0.039 0.133 572 Planarity : 0.004 0.054 604 Dihedral : 8.147 63.178 524 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.41), residues: 436 helix: 1.65 (0.31), residues: 260 sheet: 0.58 (0.87), residues: 37 loop : -1.12 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 177 HIS 0.001 0.000 HIS A 56 PHE 0.011 0.001 PHE A 225 TYR 0.020 0.001 TYR A 92 ARG 0.005 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.396 Fit side-chains REVERT: A 202 LYS cc_start: 0.8482 (mttt) cc_final: 0.8172 (mttm) REVERT: B 107 ASN cc_start: 0.8121 (t0) cc_final: 0.7907 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1706 time to fit residues: 27.5626 Evaluate side-chains 120 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3718 Z= 0.184 Angle : 0.596 7.511 5052 Z= 0.291 Chirality : 0.039 0.130 572 Planarity : 0.004 0.055 604 Dihedral : 8.085 63.088 524 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.41), residues: 436 helix: 1.59 (0.31), residues: 260 sheet: 0.64 (0.86), residues: 37 loop : -1.16 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 122 HIS 0.001 0.001 HIS A 56 PHE 0.010 0.001 PHE A 225 TYR 0.021 0.001 TYR A 92 ARG 0.003 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8408 (mttt) cc_final: 0.8136 (mttm) REVERT: B 42 TRP cc_start: 0.8475 (m100) cc_final: 0.7810 (m100) REVERT: B 83 ASN cc_start: 0.6961 (m-40) cc_final: 0.6760 (m-40) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1599 time to fit residues: 26.3161 Evaluate side-chains 120 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 HIS ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3718 Z= 0.203 Angle : 0.637 7.520 5052 Z= 0.309 Chirality : 0.040 0.132 572 Planarity : 0.004 0.057 604 Dihedral : 8.056 61.239 524 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.41), residues: 436 helix: 1.47 (0.30), residues: 263 sheet: 1.16 (0.93), residues: 29 loop : -1.19 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 122 HIS 0.004 0.001 HIS A 250 PHE 0.029 0.001 PHE A 47 TYR 0.031 0.001 TYR A 92 ARG 0.006 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.385 Fit side-chains REVERT: B 37 ILE cc_start: 0.9079 (mm) cc_final: 0.8873 (mm) REVERT: B 42 TRP cc_start: 0.8461 (m100) cc_final: 0.7980 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1491 time to fit residues: 24.0169 Evaluate side-chains 116 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 HIS A 183 GLN B 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3718 Z= 0.233 Angle : 0.639 7.339 5052 Z= 0.313 Chirality : 0.041 0.192 572 Planarity : 0.004 0.059 604 Dihedral : 8.069 60.217 524 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.26 % Allowed : 1.29 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.41), residues: 436 helix: 1.46 (0.31), residues: 260 sheet: 0.16 (0.71), residues: 50 loop : -1.30 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 122 HIS 0.002 0.001 HIS A 56 PHE 0.025 0.002 PHE A 47 TYR 0.034 0.002 TYR A 92 ARG 0.008 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8457 (mttt) cc_final: 0.8035 (mttm) REVERT: B 42 TRP cc_start: 0.8589 (m100) cc_final: 0.7907 (m100) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1578 time to fit residues: 25.5141 Evaluate side-chains 115 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3718 Z= 0.224 Angle : 0.658 8.206 5052 Z= 0.319 Chirality : 0.041 0.162 572 Planarity : 0.004 0.061 604 Dihedral : 8.025 58.911 524 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.41), residues: 436 helix: 1.56 (0.30), residues: 261 sheet: 0.21 (0.72), residues: 50 loop : -1.24 (0.63), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 93 HIS 0.002 0.000 HIS A 101 PHE 0.023 0.001 PHE A 47 TYR 0.035 0.002 TYR A 92 ARG 0.008 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.417 Fit side-chains REVERT: B 42 TRP cc_start: 0.8644 (m100) cc_final: 0.7931 (m100) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1533 time to fit residues: 23.1365 Evaluate side-chains 106 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3718 Z= 0.251 Angle : 0.677 8.445 5052 Z= 0.331 Chirality : 0.042 0.165 572 Planarity : 0.005 0.062 604 Dihedral : 8.138 59.199 524 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.41), residues: 436 helix: 1.49 (0.31), residues: 260 sheet: 0.10 (0.71), residues: 50 loop : -1.41 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 93 HIS 0.003 0.001 HIS A 250 PHE 0.024 0.002 PHE A 47 TYR 0.017 0.002 TYR B 39 ARG 0.006 0.001 ARG B 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.377 Fit side-chains REVERT: B 26 LEU cc_start: 0.7209 (mp) cc_final: 0.6829 (mp) REVERT: B 37 ILE cc_start: 0.9106 (mm) cc_final: 0.8815 (mm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1552 time to fit residues: 24.0787 Evaluate side-chains 113 residues out of total 388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137758 restraints weight = 5201.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136158 restraints weight = 6391.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137040 restraints weight = 6310.172| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3718 Z= 0.215 Angle : 0.660 8.510 5052 Z= 0.317 Chirality : 0.041 0.149 572 Planarity : 0.004 0.063 604 Dihedral : 8.165 57.697 524 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.41), residues: 436 helix: 1.58 (0.31), residues: 259 sheet: 0.05 (0.71), residues: 50 loop : -1.39 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 177 HIS 0.001 0.000 HIS A 101 PHE 0.022 0.001 PHE A 47 TYR 0.021 0.002 TYR B 39 ARG 0.005 0.001 ARG B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.87 seconds wall clock time: 22 minutes 35.57 seconds (1355.57 seconds total)