Starting phenix.real_space_refine on Wed Jan 17 14:19:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msx_23971/01_2024/7msx_23971.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 26 5.16 5 C 2359 2.51 5 N 620 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3706 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3706 Unusual residues: {' ZN': 3} Classifications: {'peptide': 473, 'undetermined': 3} Link IDs: {'PTRANS': 13, 'TRANS': 459, None: 3} Not linked: pdbres="PHE A 505 " pdbres=" ZN A 701 " Not linked: pdbres=" ZN A 701 " pdbres=" ZN A 702 " Not linked: pdbres=" ZN A 702 " pdbres=" ZN A 703 " Chain breaks: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1016 SG CYS A 143 13.882 35.673 58.737 1.00 38.05 S ATOM 1040 SG CYS A 146 12.818 36.968 62.628 1.00 47.40 S ATOM 1153 SG CYS A 161 16.687 37.445 59.660 1.00 42.84 S ATOM 1179 SG CYS A 164 15.449 34.581 62.038 1.00 44.32 S ATOM 1371 SG CYS A 190 28.609 18.258 44.496 1.00 54.40 S ATOM 1389 SG CYS A 193 30.905 15.408 45.275 1.00 70.39 S ATOM 1713 SG CYS A 236 31.982 19.316 43.189 1.00 52.65 S ATOM 136 SG CYS A 20 17.151 42.649 18.557 1.00 45.24 S ATOM 372 SG CYS A 51 16.203 45.352 15.948 1.00 45.63 S Time building chain proxies: 2.33, per 1000 atoms: 0.63 Number of scatterers: 3706 At special positions: 0 Unit cell: (57.546, 75.894, 114.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 26 16.00 O 698 8.00 N 620 7.00 C 2359 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: 1.38 Conformation dependent library (CDL) restraints added in 858.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 143 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 164 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 202 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 190 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 193 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 20 " Number of angles added : 10 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 46.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.250A pdb=" N GLY A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.562A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.732A pdb=" N LYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.671A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 492 through 503 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 184 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN A 133 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 187 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 235 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 244 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 233 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG A 246 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 231 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 248 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS A 229 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG A 222 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.678A pdb=" N LEU A 137 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.106A pdb=" N VAL A 279 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 332 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 281 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY A 334 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 283 " --> pdb=" O GLY A 334 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 492 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: 1.22 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 722 1.33 - 1.45: 924 1.45 - 1.57: 2100 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3777 Sorted by residual: bond pdb=" N PRO A 91 " pdb=" CD PRO A 91 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO A 13 " pdb=" CD PRO A 13 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 3772 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.52: 103 107.52 - 114.15: 2155 114.15 - 120.79: 1652 120.79 - 127.43: 1164 127.43 - 134.07: 29 Bond angle restraints: 5103 Sorted by residual: angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 115.21 121.46 -6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" C ALA A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 120.28 116.58 3.70 1.34e+00 5.57e-01 7.63e+00 angle pdb=" CA TRP A 432 " pdb=" CB TRP A 432 " pdb=" CG TRP A 432 " ideal model delta sigma weight residual 113.60 118.78 -5.18 1.90e+00 2.77e-01 7.44e+00 angle pdb=" C VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta sigma weight residual 111.44 109.09 2.35 9.50e-01 1.11e+00 6.11e+00 angle pdb=" C VAL A 157 " pdb=" CA VAL A 157 " pdb=" CB VAL A 157 " ideal model delta sigma weight residual 111.44 109.29 2.15 9.50e-01 1.11e+00 5.14e+00 ... (remaining 5098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 2119 14.59 - 29.17: 99 29.17 - 43.76: 21 43.76 - 58.34: 7 58.34 - 72.92: 3 Dihedral angle restraints: 2249 sinusoidal: 885 harmonic: 1364 Sorted by residual: dihedral pdb=" CA GLY A 344 " pdb=" C GLY A 344 " pdb=" N GLU A 345 " pdb=" CA GLU A 345 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA SER A 351 " pdb=" C SER A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 165.40 14.60 0 5.00e+00 4.00e-02 8.53e+00 dihedral pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 165.44 14.56 0 5.00e+00 4.00e-02 8.48e+00 ... (remaining 2246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 375 0.033 - 0.067: 91 0.067 - 0.100: 56 0.100 - 0.134: 36 0.134 - 0.167: 15 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA VAL A 186 " pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CB VAL A 186 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 570 not shown) Planarity restraints: 649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.016 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP A 432 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 464 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ASP A 464 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 464 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 465 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 463 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG A 463 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A 463 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 464 " -0.008 2.00e-02 2.50e+03 ... (remaining 646 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1457 2.89 - 3.39: 3529 3.39 - 3.89: 6079 3.89 - 4.40: 7034 4.40 - 4.90: 11643 Nonbonded interactions: 29742 Sorted by model distance: nonbonded pdb=" O GLU A 272 " pdb=" NZ LYS A 276 " model vdw 2.385 2.520 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 409 " model vdw 2.388 2.520 nonbonded pdb=" OD2 ASP A 23 " pdb=" NH1 ARG A 27 " model vdw 2.476 2.520 nonbonded pdb=" NZ LYS A 320 " pdb=" OE2 GLU A 324 " model vdw 2.561 2.520 nonbonded pdb=" N GLU A 373 " pdb=" OE1 GLU A 373 " model vdw 2.566 2.520 ... (remaining 29737 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.880 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.570 Find NCS groups from input model: 0.100 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:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.073 3777 Z= 0.519 Angle : 0.622 6.330 5103 Z= 0.397 Chirality : 0.052 0.167 573 Planarity : 0.003 0.023 649 Dihedral : 10.301 72.925 1371 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.06 (0.36), residues: 467 helix: 0.34 (0.34), residues: 180 sheet: -0.85 (0.52), residues: 74 loop : 0.34 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 432 HIS 0.001 0.000 HIS A 56 PHE 0.010 0.001 PHE A 93 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8541 (pttt) cc_final: 0.8334 (pttm) REVERT: A 499 PHE cc_start: 0.7890 (t80) cc_final: 0.7633 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2164 time to fit residues: 25.7249 Evaluate side-chains 58 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 42 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 152 GLN A 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3777 Z= 0.144 Angle : 0.471 5.328 5103 Z= 0.259 Chirality : 0.038 0.140 573 Planarity : 0.003 0.024 649 Dihedral : 4.196 20.256 502 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.97 % Allowed : 5.16 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.38), residues: 467 helix: 1.88 (0.36), residues: 181 sheet: -0.60 (0.54), residues: 74 loop : 0.39 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.011 0.001 PHE A 41 TYR 0.014 0.001 TYR A 207 ARG 0.006 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.439 Fit side-chains REVERT: A 383 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (tt0) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.2168 time to fit residues: 16.4471 Evaluate side-chains 50 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3777 Z= 0.182 Angle : 0.463 6.100 5103 Z= 0.250 Chirality : 0.039 0.152 573 Planarity : 0.003 0.028 649 Dihedral : 4.077 17.915 502 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.21 % Allowed : 7.13 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.38), residues: 467 helix: 2.17 (0.38), residues: 183 sheet: -0.66 (0.52), residues: 74 loop : 0.18 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 432 HIS 0.005 0.001 HIS A 194 PHE 0.013 0.001 PHE A 41 TYR 0.014 0.001 TYR A 207 ARG 0.005 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.451 Fit side-chains REVERT: A 383 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: A 428 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (tt) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.1738 time to fit residues: 10.6691 Evaluate side-chains 45 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3777 Z= 0.147 Angle : 0.434 5.467 5103 Z= 0.231 Chirality : 0.038 0.148 573 Planarity : 0.003 0.028 649 Dihedral : 3.906 16.515 502 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.46 % Allowed : 6.63 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.38), residues: 467 helix: 2.18 (0.38), residues: 181 sheet: -0.68 (0.53), residues: 74 loop : 0.12 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 432 HIS 0.001 0.000 HIS A 56 PHE 0.009 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.464 Fit side-chains REVERT: A 55 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6562 (pp20) REVERT: A 383 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (tt0) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.1921 time to fit residues: 12.2549 Evaluate side-chains 53 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3777 Z= 0.139 Angle : 0.408 3.878 5103 Z= 0.222 Chirality : 0.038 0.144 573 Planarity : 0.003 0.029 649 Dihedral : 3.778 15.961 502 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 7.86 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.38), residues: 467 helix: 2.17 (0.38), residues: 183 sheet: -0.66 (0.53), residues: 74 loop : 0.17 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.001 0.000 HIS A 54 PHE 0.009 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.449 Fit side-chains REVERT: A 55 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6505 (pp20) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1917 time to fit residues: 11.7644 Evaluate side-chains 48 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3777 Z= 0.326 Angle : 0.510 5.364 5103 Z= 0.276 Chirality : 0.041 0.191 573 Planarity : 0.004 0.033 649 Dihedral : 4.277 20.023 502 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 8.60 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.38), residues: 467 helix: 2.08 (0.38), residues: 183 sheet: -0.73 (0.55), residues: 74 loop : -0.03 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 243 HIS 0.004 0.001 HIS A 54 PHE 0.010 0.001 PHE A 93 TYR 0.013 0.002 TYR A 207 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.441 Fit side-chains REVERT: A 55 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6350 (pp20) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.1807 time to fit residues: 11.6711 Evaluate side-chains 50 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3777 Z= 0.160 Angle : 0.422 4.069 5103 Z= 0.231 Chirality : 0.038 0.156 573 Planarity : 0.003 0.030 649 Dihedral : 3.952 17.790 502 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.21 % Allowed : 9.83 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 467 helix: 2.02 (0.38), residues: 188 sheet: -0.66 (0.55), residues: 74 loop : 0.16 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.020 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.418 Fit side-chains REVERT: A 55 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6322 (pp20) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1880 time to fit residues: 11.2821 Evaluate side-chains 50 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3777 Z= 0.183 Angle : 0.433 4.777 5103 Z= 0.236 Chirality : 0.039 0.150 573 Planarity : 0.003 0.030 649 Dihedral : 3.962 18.161 502 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.72 % Allowed : 10.07 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.39), residues: 467 helix: 1.99 (0.38), residues: 189 sheet: -0.62 (0.56), residues: 74 loop : 0.03 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.019 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.438 Fit side-chains REVERT: A 55 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6294 (pp20) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.2013 time to fit residues: 10.9128 Evaluate side-chains 46 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.7844 > 50: distance: 106 - 108: 3.205 distance: 108 - 109: 4.920 distance: 109 - 110: 4.132 distance: 109 - 112: 3.694 distance: 110 - 111: 11.109 distance: 110 - 116: 6.217 distance: 113 - 114: 4.233 distance: 113 - 115: 5.180 distance: 116 - 117: 5.976 distance: 117 - 118: 6.881 distance: 117 - 120: 3.740 distance: 118 - 119: 11.508 distance: 118 - 127: 8.432 distance: 120 - 121: 5.619 distance: 125 - 126: 3.035 distance: 127 - 128: 7.281 distance: 128 - 129: 27.625 distance: 128 - 131: 14.743 distance: 129 - 130: 11.858 distance: 129 - 136: 22.064 distance: 131 - 132: 8.475 distance: 132 - 133: 11.080 distance: 133 - 134: 10.671 distance: 134 - 135: 9.849 distance: 136 - 137: 7.047 distance: 137 - 138: 6.410 distance: 137 - 140: 8.574 distance: 138 - 139: 7.539 distance: 138 - 143: 9.827 distance: 140 - 142: 4.128 distance: 143 - 144: 7.783 distance: 144 - 145: 10.877 distance: 144 - 147: 11.958 distance: 145 - 146: 7.801 distance: 145 - 150: 4.668 distance: 147 - 148: 4.111 distance: 147 - 149: 5.834 distance: 150 - 151: 3.690 distance: 151 - 152: 8.003 distance: 151 - 154: 16.826 distance: 152 - 153: 8.632 distance: 152 - 159: 8.497 distance: 154 - 155: 10.538 distance: 155 - 156: 9.586 distance: 156 - 157: 11.102 distance: 157 - 158: 7.717 distance: 159 - 160: 6.674 distance: 160 - 161: 7.417 distance: 161 - 162: 11.828 distance: 161 - 163: 7.107 distance: 163 - 164: 6.741 distance: 164 - 165: 6.377 distance: 165 - 166: 10.126 distance: 165 - 172: 11.124 distance: 167 - 168: 6.686 distance: 168 - 169: 14.736 distance: 169 - 170: 13.915 distance: 170 - 171: 7.009 distance: 172 - 173: 6.089 distance: 173 - 174: 11.832 distance: 173 - 176: 5.303 distance: 174 - 175: 8.118 distance: 174 - 177: 12.496