Starting phenix.real_space_refine on Sun Aug 4 02:44:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bit_44601/08_2024/9bit_44601_trim.cif" } resolution = 3.1 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= -0.001 sd= 0.046 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 3101 2.51 5 N 767 2.21 5 O 811 1.98 5 H 4734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 112": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9448 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1890 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CXN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.63 Number of scatterers: 9448 At special positions: 0 Unit cell: (87.108, 109.8, 83.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 811 8.00 N 767 7.00 C 3101 6.00 H 4734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 986.7 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 64.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 5.106A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 112 through 132 removed outlier: 3.534A pdb=" N ALA A 132 " --> pdb=" O LYS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.234A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.790A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.573A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.590A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 3.971A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.710A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.870A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.974A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.674A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.595A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.576A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.913A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.532A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.887A pdb=" N LYS A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 665 removed outlier: 3.794A pdb=" N VAL A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.209A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.308A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 96 " --> pdb=" O GLY B 118 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 810 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: 3.12 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4724 1.04 - 1.24: 632 1.24 - 1.44: 1489 1.44 - 1.64: 2676 1.64 - 1.84: 55 Bond restraints: 9576 Sorted by residual: bond pdb=" C ALA A 104 " pdb=" N ASP A 105 " ideal model delta sigma weight residual 1.335 1.287 0.048 1.36e-02 5.41e+03 1.26e+01 bond pdb=" N25 CXN A 801 " pdb=" O24 CXN A 801 " ideal model delta sigma weight residual 1.363 1.416 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" N ASP A 105 " pdb=" H ASP A 105 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C6 CXN A 801 " pdb=" C8 CXN A 801 " ideal model delta sigma weight residual 1.546 1.507 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.61e+00 ... (remaining 9571 not shown) Histogram of bond angle deviations from ideal: 84.87 - 95.13: 5 95.13 - 105.39: 86 105.39 - 115.65: 11943 115.65 - 125.90: 5144 125.90 - 136.16: 115 Bond angle restraints: 17293 Sorted by residual: angle pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 120.42 116.81 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C26 CXN A 801 " ideal model delta sigma weight residual 132.03 122.19 9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C ALA A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 120.29 124.57 -4.28 1.42e+00 4.96e-01 9.10e+00 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C23 CXN A 801 " ideal model delta sigma weight residual 124.59 133.26 -8.67 3.00e+00 1.11e-01 8.35e+00 angle pdb=" N THR A 96 " pdb=" CA THR A 96 " pdb=" C THR A 96 " ideal model delta sigma weight residual 109.81 115.47 -5.66 2.21e+00 2.05e-01 6.57e+00 ... (remaining 17288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 4246 27.03 - 54.06: 244 54.06 - 81.08: 44 81.08 - 108.11: 3 108.11 - 135.14: 4 Dihedral angle restraints: 4541 sinusoidal: 2402 harmonic: 2139 Sorted by residual: dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C52 CXN A 801 " pdb=" C5 CXN A 801 " pdb=" C6 CXN A 801 " pdb=" N7 CXN A 801 " ideal model delta sinusoidal sigma weight residual 144.67 -80.19 -135.14 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 484 0.029 - 0.057: 168 0.057 - 0.086: 57 0.086 - 0.114: 21 0.114 - 0.143: 8 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA ILE A 133 " pdb=" N ILE A 133 " pdb=" C ILE A 133 " pdb=" CB ILE A 133 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" C PRO A 97 " pdb=" CB PRO A 97 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 735 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 CXN A 801 " 0.191 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" C21 CXN A 801 " -0.042 2.00e-02 2.50e+03 pdb=" C22 CXN A 801 " -0.028 2.00e-02 2.50e+03 pdb=" N2 CXN A 801 " -0.273 2.00e-02 2.50e+03 pdb=" O21 CXN A 801 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 CXN A 801 " 0.050 2.00e-02 2.50e+03 3.67e-02 2.70e+01 pdb=" C22 CXN A 801 " -0.015 2.00e-02 2.50e+03 pdb=" C23 CXN A 801 " 0.016 2.00e-02 2.50e+03 pdb=" C26 CXN A 801 " -0.010 2.00e-02 2.50e+03 pdb=" C27 CXN A 801 " -0.058 2.00e-02 2.50e+03 pdb=" C28 CXN A 801 " -0.046 2.00e-02 2.50e+03 pdb=" N25 CXN A 801 " 0.023 2.00e-02 2.50e+03 pdb=" O24 CXN A 801 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 88 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1029 2.23 - 2.83: 20711 2.83 - 3.42: 24832 3.42 - 4.01: 33869 4.01 - 4.60: 52356 Nonbonded interactions: 132797 Sorted by model distance: nonbonded pdb=" O TRP B 53 " pdb=" HG SER B 54 " model vdw 1.642 2.450 nonbonded pdb=" O ALA A 637 " pdb=" HZ3 LYS A 642 " model vdw 1.659 2.450 nonbonded pdb=" OD1 ASP A 170 " pdb=" HH TYR A 634 " model vdw 1.670 2.450 nonbonded pdb=" O PHE A 167 " pdb="HE21 GLN A 171 " model vdw 1.676 2.450 nonbonded pdb=" OD1 ASP A 333 " pdb=" H LEU A 334 " model vdw 1.678 2.450 ... (remaining 132792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.350 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: 0.140 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.053 4842 Z= 0.191 Angle : 0.603 9.844 6583 Z= 0.321 Chirality : 0.037 0.143 738 Planarity : 0.007 0.165 814 Dihedral : 18.476 135.140 1725 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.60 % Allowed : 24.40 % Favored : 74.00 % 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: -0.05 (0.36), residues: 589 helix: 1.20 (0.29), residues: 343 sheet: -1.84 (0.65), residues: 59 loop : -1.72 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.008 0.001 PHE A 48 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7198 (mt0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.3436 time to fit residues: 35.1832 Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 607 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4842 Z= 0.205 Angle : 0.567 5.550 6583 Z= 0.297 Chirality : 0.038 0.153 738 Planarity : 0.004 0.047 814 Dihedral : 11.775 131.184 687 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.80 % Allowed : 24.20 % Favored : 74.00 % 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: 0.23 (0.36), residues: 589 helix: 1.58 (0.28), residues: 345 sheet: -2.23 (0.61), residues: 59 loop : -1.78 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.017 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7019 (pm20) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.3461 time to fit residues: 30.9899 Evaluate side-chains 71 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4842 Z= 0.287 Angle : 0.587 5.498 6583 Z= 0.308 Chirality : 0.039 0.150 738 Planarity : 0.005 0.051 814 Dihedral : 11.694 139.472 680 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.00 % Allowed : 24.00 % Favored : 74.00 % 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: 0.13 (0.35), residues: 589 helix: 1.53 (0.28), residues: 344 sheet: -2.10 (0.62), residues: 57 loop : -1.96 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.024 0.002 PHE A 48 TYR 0.014 0.002 TYR A 634 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7010 (pm20) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.3440 time to fit residues: 31.8948 Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4842 Z= 0.245 Angle : 0.564 5.147 6583 Z= 0.296 Chirality : 0.039 0.149 738 Planarity : 0.005 0.049 814 Dihedral : 11.356 137.193 676 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.20 % Allowed : 23.40 % Favored : 74.40 % 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: 0.16 (0.35), residues: 589 helix: 1.56 (0.28), residues: 346 sheet: -2.15 (0.61), residues: 57 loop : -1.98 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.008 0.001 HIS A 291 PHE 0.020 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.002 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6996 (pm20) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.3760 time to fit residues: 32.3850 Evaluate side-chains 69 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4842 Z= 0.294 Angle : 0.586 5.279 6583 Z= 0.309 Chirality : 0.040 0.149 738 Planarity : 0.005 0.049 814 Dihedral : 11.416 138.375 676 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.40 % Allowed : 23.80 % Favored : 73.80 % 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: 0.09 (0.35), residues: 589 helix: 1.51 (0.28), residues: 344 sheet: -2.15 (0.62), residues: 57 loop : -1.98 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.007 0.001 HIS A 291 PHE 0.023 0.002 PHE A 48 TYR 0.014 0.002 TYR A 634 ARG 0.005 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (ttp-170) REVERT: B 112 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7000 (pm20) outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.3437 time to fit residues: 32.2151 Evaluate side-chains 76 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4842 Z= 0.160 Angle : 0.528 4.765 6583 Z= 0.277 Chirality : 0.037 0.146 738 Planarity : 0.004 0.048 814 Dihedral : 11.275 135.095 676 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.00 % Allowed : 23.00 % Favored : 74.00 % 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: 0.36 (0.36), residues: 589 helix: 1.74 (0.28), residues: 348 sheet: -2.07 (0.62), residues: 57 loop : -1.97 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.007 0.001 HIS A 291 PHE 0.015 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.005 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7672 (mmm) REVERT: B 45 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: B 112 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6958 (pm20) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.3368 time to fit residues: 32.5367 Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4842 Z= 0.181 Angle : 0.525 4.862 6583 Z= 0.276 Chirality : 0.037 0.147 738 Planarity : 0.004 0.047 814 Dihedral : 11.240 136.103 676 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.80 % Allowed : 22.60 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.36), residues: 589 helix: 1.77 (0.28), residues: 348 sheet: -1.98 (0.63), residues: 57 loop : -1.90 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 PHE 0.015 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.005 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 266 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6248 (mtm110) REVERT: A 311 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: A 404 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.3122 (pmm) REVERT: B 45 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7895 (ttp-170) REVERT: B 112 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7000 (pm20) outliers start: 14 outliers final: 7 residues processed: 70 average time/residue: 0.3717 time to fit residues: 33.3094 Evaluate side-chains 74 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4842 Z= 0.186 Angle : 0.527 4.920 6583 Z= 0.277 Chirality : 0.038 0.147 738 Planarity : 0.004 0.048 814 Dihedral : 11.226 135.407 676 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.80 % Allowed : 22.20 % Favored : 75.00 % 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: 0.48 (0.36), residues: 589 helix: 1.83 (0.28), residues: 345 sheet: -1.99 (0.63), residues: 57 loop : -1.87 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 PHE 0.016 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.005 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 266 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6294 (mtm110) REVERT: A 311 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: A 404 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.3223 (pmm) REVERT: B 112 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6997 (pm20) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.3875 time to fit residues: 35.3016 Evaluate side-chains 73 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4842 Z= 0.221 Angle : 0.541 4.977 6583 Z= 0.285 Chirality : 0.038 0.149 738 Planarity : 0.005 0.049 814 Dihedral : 11.245 135.866 676 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.60 % Allowed : 22.20 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.36), residues: 589 helix: 1.77 (0.28), residues: 345 sheet: -2.02 (0.64), residues: 57 loop : -1.89 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 PHE 0.018 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 266 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6332 (mtm110) REVERT: A 311 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7735 (mmm) REVERT: A 404 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.3300 (pmm) REVERT: B 112 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6994 (pm20) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.3509 time to fit residues: 31.6058 Evaluate side-chains 75 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4842 Z= 0.264 Angle : 0.564 5.231 6583 Z= 0.297 Chirality : 0.039 0.152 738 Planarity : 0.005 0.050 814 Dihedral : 11.308 136.110 676 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.20 % Allowed : 21.80 % Favored : 75.00 % 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: 0.24 (0.35), residues: 589 helix: 1.65 (0.28), residues: 344 sheet: -2.13 (0.63), residues: 57 loop : -1.95 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 PHE 0.020 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.007 0.001 ARG A 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: A 404 MET cc_start: 0.4650 (OUTLIER) cc_final: 0.3325 (pmm) REVERT: B 112 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6996 (pm20) outliers start: 16 outliers final: 12 residues processed: 72 average time/residue: 0.3480 time to fit residues: 32.3306 Evaluate side-chains 78 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.164340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137456 restraints weight = 14838.113| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.60 r_work: 0.3357 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4842 Z= 0.178 Angle : 0.527 4.807 6583 Z= 0.278 Chirality : 0.037 0.148 738 Planarity : 0.004 0.048 814 Dihedral : 11.222 134.153 676 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.80 % Allowed : 22.00 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.36), residues: 589 helix: 1.83 (0.28), residues: 345 sheet: -2.00 (0.64), residues: 57 loop : -1.87 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 PHE 0.015 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.53 seconds wall clock time: 53 minutes 53.66 seconds (3233.66 seconds total)