Starting phenix.real_space_refine on Tue Feb 13 07:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/02_2024/7da5_30623.pdb" } resolution = 3.3 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= 0.004 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2611 2.51 5 N 683 2.21 5 O 694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4013 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1167 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 2.79, per 1000 atoms: 0.70 Number of scatterers: 4013 At special positions: 0 Unit cell: (102.883, 54.8145, 114.689, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 694 8.00 N 683 7.00 C 2611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.88 Conformation dependent library (CDL) restraints added in 860.7 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 62.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 34 removed outlier: 3.986A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 55 through 84 removed outlier: 5.568A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 109 through 139 Proline residue: A 130 - end of helix removed outlier: 3.505A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.441A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 192 removed outlier: 3.966A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 290 removed outlier: 6.062A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 321 removed outlier: 4.294A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.933A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 330 through 346 removed outlier: 4.102A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 removed outlier: 3.995A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 415 removed outlier: 4.353A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix Proline residue: A 406 - end of helix removed outlier: 4.590A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.771A pdb=" N TYR A 423 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 204 through 238 Proline residue: B 211 - end of helix removed outlier: 3.562A pdb=" N THR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 4.542A pdb=" N VAL B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.449A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 632 1.28 - 1.41: 1071 1.41 - 1.54: 2303 1.54 - 1.68: 58 1.68 - 1.81: 38 Bond restraints: 4102 Sorted by residual: bond pdb=" C PHE A 36 " pdb=" O PHE A 36 " ideal model delta sigma weight residual 1.238 1.144 0.094 1.28e-02 6.10e+03 5.39e+01 bond pdb=" CA ALA A 35 " pdb=" CB ALA A 35 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.02e-02 9.61e+03 2.92e+01 bond pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 1.474 1.539 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.474 1.535 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CA VAL B 131 " pdb=" C VAL B 131 " ideal model delta sigma weight residual 1.524 1.557 -0.033 8.30e-03 1.45e+04 1.61e+01 ... (remaining 4097 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.19: 82 105.19 - 112.39: 1973 112.39 - 119.60: 1393 119.60 - 126.80: 2100 126.80 - 134.01: 54 Bond angle restraints: 5602 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.99 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 111.50 98.10 13.40 1.40e+00 5.10e-01 9.16e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.09 12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" C TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta sigma weight residual 111.45 125.90 -14.45 1.72e+00 3.38e-01 7.06e+01 angle pdb=" C PHE A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta sigma weight residual 119.84 129.71 -9.87 1.25e+00 6.40e-01 6.24e+01 ... (remaining 5597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2054 17.50 - 35.00: 208 35.00 - 52.50: 61 52.50 - 70.00: 11 70.00 - 87.50: 3 Dihedral angle restraints: 2337 sinusoidal: 675 harmonic: 1662 Sorted by residual: dihedral pdb=" C TYR A 34 " pdb=" N TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta harmonic sigma weight residual -122.60 -142.16 19.56 0 2.50e+00 1.60e-01 6.12e+01 dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.09 17.09 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.10 -15.70 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 2334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 610 0.130 - 0.259: 37 0.259 - 0.389: 7 0.389 - 0.518: 4 0.518 - 0.648: 3 Chirality restraints: 661 Sorted by residual: chirality pdb=" CA TYR A 34 " pdb=" N TYR A 34 " pdb=" C TYR A 34 " pdb=" CB TYR A 34 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 658 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.063 2.00e-02 2.50e+03 5.57e-02 5.44e+01 pdb=" CG PHE A 36 " 0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 36 " 0.032 2.00e-02 2.50e+03 6.63e-02 4.40e+01 pdb=" C PHE A 36 " -0.115 2.00e-02 2.50e+03 pdb=" O PHE A 36 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 37 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 131 " 0.117 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 132 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.067 5.00e-02 4.00e+02 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 15 2.32 - 2.96: 2199 2.96 - 3.61: 5766 3.61 - 4.25: 8424 4.25 - 4.90: 14144 Nonbonded interactions: 30548 Sorted by model distance: nonbonded pdb=" O ILE A 171 " pdb=" NE ARG B 203 " model vdw 1.673 2.520 nonbonded pdb=" CB HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 1.936 3.520 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 1.959 2.440 nonbonded pdb=" CG2 THR A 54 " pdb=" OE2 GLU A 57 " model vdw 2.028 3.460 nonbonded pdb=" O PRO A 74 " pdb=" OG SER A 77 " model vdw 2.058 2.440 ... (remaining 30543 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 3.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 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 : 0.008 0.094 4102 Z= 0.539 Angle : 1.210 14.454 5602 Z= 0.816 Chirality : 0.087 0.648 661 Planarity : 0.010 0.164 718 Dihedral : 16.471 87.496 1281 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.06 % Favored : 90.60 % Rotamer: Outliers : 10.06 % Allowed : 18.60 % Favored : 71.34 % Cbeta Deviations : 1.89 % Peptide Plane: Cis-proline : 11.11 % 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: -3.63 (0.31), residues: 585 helix: -2.39 (0.24), residues: 342 sheet: 0.31 (0.53), residues: 94 loop : -3.80 (0.40), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.001 0.000 HIS A 292 PHE 0.129 0.002 PHE A 36 TYR 0.047 0.002 TYR A 34 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 53 time to evaluate : 0.425 Fit side-chains REVERT: A 82 LYS cc_start: 0.7178 (tttt) cc_final: 0.6594 (mmtt) REVERT: B 115 HIS cc_start: 0.0400 (OUTLIER) cc_final: 0.0011 (p90) outliers start: 33 outliers final: 17 residues processed: 79 average time/residue: 0.2074 time to fit residues: 19.7651 Evaluate side-chains 57 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4102 Z= 0.216 Angle : 0.679 6.783 5602 Z= 0.355 Chirality : 0.042 0.187 661 Planarity : 0.006 0.071 718 Dihedral : 6.654 49.642 646 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.18 % Allowed : 17.07 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.63 (0.34), residues: 585 helix: -0.61 (0.28), residues: 349 sheet: 0.84 (0.52), residues: 101 loop : -3.64 (0.45), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.002 0.001 HIS A 344 PHE 0.035 0.002 PHE A 332 TYR 0.025 0.002 TYR A 34 ARG 0.007 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.339 Fit side-chains REVERT: A 27 PHE cc_start: 0.7745 (t80) cc_final: 0.7493 (t80) REVERT: A 273 MET cc_start: 0.7879 (ppp) cc_final: 0.7655 (tmm) outliers start: 17 outliers final: 9 residues processed: 66 average time/residue: 0.1359 time to fit residues: 11.8061 Evaluate side-chains 50 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 50.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4102 Z= 0.343 Angle : 0.752 8.073 5602 Z= 0.405 Chirality : 0.047 0.171 661 Planarity : 0.007 0.075 718 Dihedral : 5.957 43.063 626 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.69 % Favored : 92.14 % Rotamer: Outliers : 9.15 % Allowed : 18.60 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.34 (0.34), residues: 585 helix: -0.55 (0.27), residues: 351 sheet: 1.38 (0.53), residues: 96 loop : -3.23 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 18 HIS 0.007 0.002 HIS B 205 PHE 0.020 0.002 PHE A 332 TYR 0.023 0.003 TYR A 34 ARG 0.008 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.483 Fit side-chains REVERT: A 273 MET cc_start: 0.8166 (ppp) cc_final: 0.7893 (tmm) outliers start: 30 outliers final: 14 residues processed: 88 average time/residue: 0.1163 time to fit residues: 13.8363 Evaluate side-chains 79 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4102 Z= 0.199 Angle : 0.648 7.379 5602 Z= 0.329 Chirality : 0.041 0.139 661 Planarity : 0.005 0.071 718 Dihedral : 5.290 40.533 626 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.57 % Allowed : 21.95 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.50 (0.36), residues: 585 helix: 0.17 (0.28), residues: 351 sheet: 1.53 (0.52), residues: 96 loop : -2.92 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 344 PHE 0.017 0.001 PHE A 27 TYR 0.014 0.002 TYR A 34 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.487 Fit side-chains REVERT: A 27 PHE cc_start: 0.7707 (t80) cc_final: 0.7462 (t80) outliers start: 15 outliers final: 8 residues processed: 78 average time/residue: 0.1572 time to fit residues: 15.4061 Evaluate side-chains 65 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 50.0000 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4102 Z= 0.330 Angle : 0.734 9.539 5602 Z= 0.380 Chirality : 0.045 0.158 661 Planarity : 0.006 0.073 718 Dihedral : 5.507 41.252 625 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 7.01 % Allowed : 21.65 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 585 helix: 0.17 (0.28), residues: 348 sheet: 1.49 (0.54), residues: 96 loop : -2.90 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 174 HIS 0.006 0.002 HIS A 344 PHE 0.018 0.002 PHE A 27 TYR 0.018 0.003 TYR A 34 ARG 0.005 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.454 Fit side-chains REVERT: A 27 PHE cc_start: 0.7852 (t80) cc_final: 0.7496 (t80) REVERT: A 140 TYR cc_start: 0.4634 (m-10) cc_final: 0.4113 (t80) REVERT: A 151 MET cc_start: 0.7254 (tpp) cc_final: 0.7032 (tpp) outliers start: 23 outliers final: 13 residues processed: 73 average time/residue: 0.1133 time to fit residues: 11.4403 Evaluate side-chains 70 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 40 optimal weight: 50.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4102 Z= 0.202 Angle : 0.652 8.922 5602 Z= 0.328 Chirality : 0.042 0.158 661 Planarity : 0.005 0.071 718 Dihedral : 5.144 40.855 625 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.79 % Allowed : 23.17 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.10 (0.36), residues: 585 helix: 0.54 (0.28), residues: 348 sheet: 1.50 (0.53), residues: 96 loop : -2.69 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 27 TYR 0.014 0.001 TYR A 34 ARG 0.005 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.409 Fit side-chains REVERT: A 140 TYR cc_start: 0.4512 (m-10) cc_final: 0.4115 (t80) REVERT: B 203 ARG cc_start: 0.3107 (mtt90) cc_final: 0.2855 (mtt90) outliers start: 19 outliers final: 13 residues processed: 70 average time/residue: 0.1611 time to fit residues: 14.1925 Evaluate side-chains 66 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4102 Z= 0.291 Angle : 0.707 9.588 5602 Z= 0.366 Chirality : 0.044 0.171 661 Planarity : 0.006 0.072 718 Dihedral : 5.397 41.262 625 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.01 % Allowed : 22.56 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.32 (0.35), residues: 585 helix: 0.35 (0.28), residues: 347 sheet: 1.40 (0.55), residues: 96 loop : -2.70 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 174 HIS 0.005 0.001 HIS A 344 PHE 0.015 0.002 PHE A 27 TYR 0.022 0.002 TYR A 34 ARG 0.004 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 0.459 Fit side-chains REVERT: A 140 TYR cc_start: 0.4603 (m-10) cc_final: 0.4005 (t80) REVERT: A 273 MET cc_start: 0.8370 (tmm) cc_final: 0.8154 (ppp) outliers start: 23 outliers final: 16 residues processed: 77 average time/residue: 0.1243 time to fit residues: 12.7175 Evaluate side-chains 75 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 4102 Z= 0.392 Angle : 0.810 12.184 5602 Z= 0.428 Chirality : 0.047 0.187 661 Planarity : 0.006 0.081 718 Dihedral : 5.975 42.442 625 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 7.01 % Allowed : 24.09 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.93 (0.34), residues: 585 helix: -0.13 (0.27), residues: 347 sheet: 1.23 (0.56), residues: 88 loop : -2.79 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 174 HIS 0.006 0.002 HIS A 344 PHE 0.023 0.002 PHE A 43 TYR 0.022 0.003 TYR A 34 ARG 0.003 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.463 Fit side-chains REVERT: B 203 ARG cc_start: 0.3552 (mtt90) cc_final: 0.3095 (mtt90) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.1303 time to fit residues: 13.8042 Evaluate side-chains 79 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.0370 chunk 33 optimal weight: 0.0020 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 50.0000 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4102 Z= 0.203 Angle : 0.665 8.874 5602 Z= 0.335 Chirality : 0.042 0.161 661 Planarity : 0.005 0.071 718 Dihedral : 5.227 39.671 625 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.57 % Allowed : 27.44 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 585 helix: 0.56 (0.29), residues: 347 sheet: 1.47 (0.57), residues: 87 loop : -2.81 (0.45), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 60 HIS 0.003 0.001 HIS A 344 PHE 0.031 0.002 PHE A 43 TYR 0.021 0.001 TYR A 34 ARG 0.003 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.435 Fit side-chains REVERT: A 138 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6977 (t80) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.1377 time to fit residues: 13.7076 Evaluate side-chains 70 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4102 Z= 0.209 Angle : 0.691 9.850 5602 Z= 0.339 Chirality : 0.041 0.161 661 Planarity : 0.005 0.067 718 Dihedral : 5.087 40.734 625 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.27 % Allowed : 28.05 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.03 (0.36), residues: 585 helix: 0.71 (0.29), residues: 348 sheet: 1.64 (0.58), residues: 87 loop : -2.80 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.003 0.001 HIS A 344 PHE 0.013 0.001 PHE A 274 TYR 0.022 0.002 TYR A 287 ARG 0.004 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.451 Fit side-chains REVERT: A 138 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6946 (t80) outliers start: 14 outliers final: 13 residues processed: 68 average time/residue: 0.1491 time to fit residues: 13.0554 Evaluate side-chains 68 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.206370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.171780 restraints weight = 5849.435| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.78 r_work: 0.4081 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4102 Z= 0.317 Angle : 0.779 14.884 5602 Z= 0.394 Chirality : 0.045 0.176 661 Planarity : 0.006 0.074 718 Dihedral : 5.578 40.714 625 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.49 % Allowed : 27.74 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 585 helix: 0.39 (0.28), residues: 348 sheet: 1.32 (0.58), residues: 87 loop : -2.94 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.005 0.002 HIS A 344 PHE 0.018 0.002 PHE A 263 TYR 0.023 0.002 TYR A 34 ARG 0.005 0.001 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1182.86 seconds wall clock time: 21 minutes 59.36 seconds (1319.36 seconds total)