Starting phenix.real_space_refine on Wed Feb 14 08:12:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csz_26976/02_2024/8csz_26976.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 236 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 4741 2.51 5 N 1654 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 19": "NH1" <-> "NH2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 473": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3950 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 67} Link IDs: {'rna2p': 25, 'rna3p': 158} Chain breaks: 2 Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 661 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "E" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2125 SG CYS D 265 82.445 57.202 49.318 1.00 89.87 S Time building chain proxies: 5.98, per 1000 atoms: 0.67 Number of scatterers: 8948 At special positions: 0 Unit cell: (99.51, 111.28, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 236 15.00 Mg 2 11.99 O 2287 8.00 N 1654 7.00 C 4741 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: 5.06 Conformation dependent library (CDL) restraints added in 835.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 265 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 268 " 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 34.8% alpha, 17.8% beta 82 base pairs and 139 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'D' and resid 21 through 29 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.413A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 removed outlier: 3.723A pdb=" N ILE D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 265 through 275 Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.715A pdb=" N GLU D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.870A pdb=" N VAL D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.692A pdb=" N TYR D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 423 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 17 removed outlier: 5.180A pdb=" N MET D 15 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 6 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 3.988A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 79 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.593A pdb=" N GLN D 432 " --> pdb=" O HIS D 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 392 through 395 removed outlier: 5.883A pdb=" N LEU D 393 " --> pdb=" O MET D 389 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET D 389 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 395 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 386 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.997A pdb=" N GLY D 460 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 469 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER D 458 " --> pdb=" O PHE D 469 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 471 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER D 456 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 444 " --> pdb=" O LEU D 485 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 429 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 139 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 5.33 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: 1542 1.33 - 1.45: 3518 1.45 - 1.57: 4051 1.57 - 1.69: 467 1.69 - 1.80: 42 Bond restraints: 9620 Sorted by residual: bond pdb=" O5' G C 172 " pdb=" C5' G C 172 " ideal model delta sigma weight residual 1.420 1.443 -0.023 1.50e-02 4.44e+03 2.29e+00 bond pdb=" O5' A C 78 " pdb=" C5' A C 78 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.73e+00 bond pdb=" CB ARG D 101 " pdb=" CG ARG D 101 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" N ASN D 203 " pdb=" CA ASN D 203 " ideal model delta sigma weight residual 1.463 1.451 0.011 9.30e-03 1.16e+04 1.47e+00 bond pdb=" O5' U C 205 " pdb=" C5' U C 205 " ideal model delta sigma weight residual 1.420 1.438 -0.018 1.50e-02 4.44e+03 1.47e+00 ... (remaining 9615 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 1307 105.87 - 112.91: 5429 112.91 - 119.95: 3368 119.95 - 126.99: 3412 126.99 - 134.03: 586 Bond angle restraints: 14102 Sorted by residual: angle pdb=" O3' DG E 127 " pdb=" C3' DG E 127 " pdb=" C2' DG E 127 " ideal model delta sigma weight residual 111.50 104.54 6.96 1.50e+00 4.44e-01 2.15e+01 angle pdb=" C4' U C 206 " pdb=" C3' U C 206 " pdb=" O3' U C 206 " ideal model delta sigma weight residual 109.40 114.83 -5.43 1.50e+00 4.44e-01 1.31e+01 angle pdb=" O3' DA B 10 " pdb=" C3' DA B 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 111.50 106.22 5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C3' A C 128 " pdb=" O3' A C 128 " pdb=" P U C 129 " ideal model delta sigma weight residual 120.20 124.99 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C4' A C 128 " pdb=" C3' A C 128 " pdb=" O3' A C 128 " ideal model delta sigma weight residual 109.40 114.19 -4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 14097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 5157 34.92 - 69.84: 614 69.84 - 104.77: 59 104.77 - 139.69: 6 139.69 - 174.61: 8 Dihedral angle restraints: 5844 sinusoidal: 4409 harmonic: 1435 Sorted by residual: dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 40.92 159.08 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C C 94 " pdb=" C1' C C 94 " pdb=" N1 C C 94 " pdb=" C2 C C 94 " ideal model delta sinusoidal sigma weight residual 232.00 57.39 174.61 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U C 107 " pdb=" C1' U C 107 " pdb=" N1 U C 107 " pdb=" C2 U C 107 " ideal model delta sinusoidal sigma weight residual -128.00 39.42 -167.42 1 1.70e+01 3.46e-03 6.56e+01 ... (remaining 5841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1544 0.062 - 0.124: 138 0.124 - 0.185: 15 0.185 - 0.247: 7 0.247 - 0.309: 1 Chirality restraints: 1705 Sorted by residual: chirality pdb=" C3' U C 206 " pdb=" C4' U C 206 " pdb=" O3' U C 206 " pdb=" C2' U C 206 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' A C 78 " pdb=" C4' A C 78 " pdb=" O3' A C 78 " pdb=" C2' A C 78 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C3' A C 128 " pdb=" C4' A C 128 " pdb=" O3' A C 128 " pdb=" C2' A C 128 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1702 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 122 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.31e+00 pdb=" N9 A C 122 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A C 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A C 122 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A C 122 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 122 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 122 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 122 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 122 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A C 122 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 91 " -0.032 2.00e-02 2.50e+03 1.40e-02 5.86e+00 pdb=" N9 G C 91 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G C 91 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 91 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 91 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G C 91 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 91 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G C 91 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 127 " -0.030 2.00e-02 2.50e+03 1.56e-02 5.47e+00 pdb=" N1 C C 127 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C C 127 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C C 127 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 127 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C C 127 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 127 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C C 127 " 0.003 2.00e-02 2.50e+03 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 61 2.55 - 3.14: 6562 3.14 - 3.72: 16549 3.72 - 4.31: 23135 4.31 - 4.90: 32429 Nonbonded interactions: 78736 Sorted by model distance: nonbonded pdb=" ND1 HIS D 245 " pdb="MG MG D 501 " model vdw 1.962 2.250 nonbonded pdb=" NE2 HIS D 269 " pdb="MG MG D 501 " model vdw 2.018 2.250 nonbonded pdb=" OP2 DC E 111 " pdb="MG MG D 502 " model vdw 2.021 2.170 nonbonded pdb=" ND1 HIS D 273 " pdb="MG MG D 501 " model vdw 2.071 2.250 nonbonded pdb=" O2' U C 180 " pdb=" OP1 C C 181 " model vdw 2.127 2.440 ... (remaining 78731 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: 2.960 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: 5.120 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.005 0.037 9620 Z= 0.317 Angle : 0.672 7.704 14102 Z= 0.385 Chirality : 0.040 0.309 1705 Planarity : 0.004 0.053 938 Dihedral : 23.812 174.610 4922 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.97 (0.37), residues: 492 helix: 0.82 (0.42), residues: 152 sheet: -1.55 (0.65), residues: 65 loop : -1.27 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 478 HIS 0.007 0.001 HIS D 273 PHE 0.007 0.001 PHE D 453 TYR 0.011 0.002 TYR D 340 ARG 0.008 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.695 Fit side-chains REVERT: D 353 ASP cc_start: 0.7944 (m-30) cc_final: 0.7581 (p0) REVERT: D 403 ASP cc_start: 0.7862 (m-30) cc_final: 0.7354 (m-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.3297 time to fit residues: 15.3776 Evaluate side-chains 27 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 ASN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9620 Z= 0.401 Angle : 0.678 11.392 14102 Z= 0.363 Chirality : 0.040 0.295 1705 Planarity : 0.005 0.046 938 Dihedral : 24.847 175.735 3920 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.71 % Allowed : 6.12 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.84 (0.37), residues: 492 helix: 0.94 (0.42), residues: 152 sheet: -1.40 (0.64), residues: 65 loop : -1.22 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 161 HIS 0.006 0.001 HIS D 269 PHE 0.010 0.001 PHE D 453 TYR 0.012 0.002 TYR D 5 ARG 0.005 0.001 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.628 Fit side-chains REVERT: D 208 ARG cc_start: 0.7299 (mpp80) cc_final: 0.6608 (mtp180) REVERT: D 273 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7476 (t-170) REVERT: D 353 ASP cc_start: 0.8009 (m-30) cc_final: 0.7650 (p0) REVERT: D 403 ASP cc_start: 0.7900 (m-30) cc_final: 0.7103 (m-30) outliers start: 3 outliers final: 1 residues processed: 31 average time/residue: 0.3091 time to fit residues: 12.8641 Evaluate side-chains 30 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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: 0.8505 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9620 Z= 0.330 Angle : 0.628 9.979 14102 Z= 0.336 Chirality : 0.038 0.260 1705 Planarity : 0.004 0.043 938 Dihedral : 24.748 177.495 3920 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.65 % Allowed : 7.53 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.69 (0.37), residues: 492 helix: 1.10 (0.42), residues: 152 sheet: -1.29 (0.66), residues: 55 loop : -1.18 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 478 HIS 0.004 0.001 HIS D 269 PHE 0.008 0.001 PHE D 453 TYR 0.011 0.002 TYR D 5 ARG 0.003 0.001 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.661 Fit side-chains REVERT: D 353 ASP cc_start: 0.7997 (m-30) cc_final: 0.7656 (p0) outliers start: 7 outliers final: 3 residues processed: 34 average time/residue: 0.2918 time to fit residues: 13.3893 Evaluate side-chains 31 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 HIS D 428 HIS ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9620 Z= 0.151 Angle : 0.540 8.022 14102 Z= 0.292 Chirality : 0.033 0.195 1705 Planarity : 0.004 0.044 938 Dihedral : 24.592 179.222 3920 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.65 % Allowed : 8.47 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.22 (0.37), residues: 492 helix: 1.58 (0.42), residues: 154 sheet: -0.83 (0.68), residues: 55 loop : -1.01 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 478 HIS 0.003 0.001 HIS D 273 PHE 0.007 0.001 PHE D 124 TYR 0.009 0.001 TYR D 340 ARG 0.003 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.675 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.2970 time to fit residues: 15.7755 Evaluate side-chains 31 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 overall best weight: 2.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9620 Z= 0.326 Angle : 0.608 8.176 14102 Z= 0.326 Chirality : 0.037 0.245 1705 Planarity : 0.004 0.041 938 Dihedral : 24.579 179.733 3920 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.65 % Allowed : 10.12 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.37), residues: 492 helix: 1.33 (0.42), residues: 155 sheet: -1.11 (0.67), residues: 55 loop : -1.05 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.003 0.001 HIS D 399 PHE 0.009 0.001 PHE D 453 TYR 0.010 0.001 TYR D 5 ARG 0.004 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.779 Fit side-chains REVERT: D 208 ARG cc_start: 0.7172 (mpp80) cc_final: 0.6394 (mtp180) outliers start: 7 outliers final: 7 residues processed: 39 average time/residue: 0.2637 time to fit residues: 14.0724 Evaluate side-chains 36 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.2444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9620 Z= 0.193 Angle : 0.550 8.039 14102 Z= 0.298 Chirality : 0.033 0.193 1705 Planarity : 0.004 0.042 938 Dihedral : 24.494 179.947 3920 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.41 % Allowed : 11.53 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.19 (0.38), residues: 492 helix: 1.54 (0.42), residues: 155 sheet: -0.92 (0.69), residues: 55 loop : -0.93 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 478 HIS 0.002 0.001 HIS D 273 PHE 0.007 0.001 PHE D 198 TYR 0.010 0.001 TYR D 5 ARG 0.002 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.660 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 34 average time/residue: 0.2676 time to fit residues: 12.5544 Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9620 Z= 0.158 Angle : 0.529 8.013 14102 Z= 0.288 Chirality : 0.032 0.186 1705 Planarity : 0.004 0.042 938 Dihedral : 24.446 179.997 3920 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.65 % Allowed : 12.00 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.01 (0.38), residues: 492 helix: 1.70 (0.42), residues: 155 sheet: -0.70 (0.70), residues: 55 loop : -0.85 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 478 HIS 0.002 0.001 HIS D 233 PHE 0.007 0.001 PHE D 198 TYR 0.009 0.001 TYR D 340 ARG 0.004 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.608 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 33 average time/residue: 0.2667 time to fit residues: 12.0678 Evaluate side-chains 33 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8544 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 9620 Z= 0.498 Angle : 0.704 8.431 14102 Z= 0.374 Chirality : 0.042 0.314 1705 Planarity : 0.005 0.042 938 Dihedral : 24.563 179.906 3920 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.88 % Allowed : 11.29 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.62 (0.37), residues: 492 helix: 1.12 (0.42), residues: 153 sheet: -1.02 (0.62), residues: 65 loop : -1.17 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.005 0.002 HIS D 294 PHE 0.012 0.002 PHE D 453 TYR 0.015 0.002 TYR D 5 ARG 0.004 0.001 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.678 Fit side-chains REVERT: D 208 ARG cc_start: 0.7302 (mpp80) cc_final: 0.6605 (mtp180) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.2943 time to fit residues: 14.3153 Evaluate side-chains 35 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9620 Z= 0.225 Angle : 0.566 8.242 14102 Z= 0.306 Chirality : 0.035 0.219 1705 Planarity : 0.004 0.039 938 Dihedral : 24.450 179.674 3920 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.88 % Allowed : 12.00 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.28 (0.38), residues: 492 helix: 1.40 (0.42), residues: 155 sheet: -0.97 (0.70), residues: 55 loop : -0.94 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 478 HIS 0.002 0.001 HIS D 273 PHE 0.007 0.001 PHE D 79 TYR 0.010 0.001 TYR D 484 ARG 0.003 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.737 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 32 average time/residue: 0.2820 time to fit residues: 12.4029 Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9620 Z= 0.255 Angle : 0.572 8.248 14102 Z= 0.308 Chirality : 0.035 0.220 1705 Planarity : 0.004 0.039 938 Dihedral : 24.422 179.975 3920 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.88 % Allowed : 12.00 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.26 (0.38), residues: 492 helix: 1.42 (0.42), residues: 155 sheet: -0.97 (0.70), residues: 55 loop : -0.93 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 278 HIS 0.003 0.001 HIS D 273 PHE 0.007 0.001 PHE D 453 TYR 0.011 0.001 TYR D 5 ARG 0.002 0.000 ARG D 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.644 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 32 average time/residue: 0.2849 time to fit residues: 12.5010 Evaluate side-chains 34 residues out of total 428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.057868 restraints weight = 23701.126| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.71 r_work: 0.2759 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9620 Z= 0.328 Angle : 0.605 8.342 14102 Z= 0.324 Chirality : 0.037 0.259 1705 Planarity : 0.004 0.038 938 Dihedral : 24.455 179.698 3920 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.12 % Allowed : 11.76 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.38), residues: 492 helix: 1.34 (0.42), residues: 153 sheet: -0.84 (0.64), residues: 65 loop : -1.09 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.003 0.001 HIS D 273 PHE 0.009 0.001 PHE D 453 TYR 0.012 0.002 TYR D 5 ARG 0.003 0.000 ARG D 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.08 seconds wall clock time: 31 minutes 32.86 seconds (1892.86 seconds total)