Starting phenix.real_space_refine on Sat Apr 6 07:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pmp_17763/04_2024/8pmp_17763_updated.pdb" } resolution = 3.43 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 4820 2.51 5 N 1291 2.21 5 O 1396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "B TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "D GLU 858": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7554 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6112 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 706} Chain breaks: 2 Chain: "B" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1237 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 172 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.57 Number of scatterers: 7554 At special positions: 0 Unit cell: (85.578, 94.807, 111.587, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 3 15.00 O 1396 8.00 N 1291 7.00 C 4820 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: 2.85 Conformation dependent library (CDL) restraints added in 1.3 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 1 sheets defined 62.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 80 through 96 removed outlier: 5.906A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR A 86 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.086A pdb=" N THR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 205 Proline residue: A 178 - end of helix removed outlier: 6.830A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 228 through 241 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.651A pdb=" N PHE A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 4.911A pdb=" N ASP A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 471 through 476 removed outlier: 4.529A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 635 through 675 Processing helix chain 'A' and resid 687 through 731 Processing helix chain 'A' and resid 738 through 768 removed outlier: 5.737A pdb=" N GLN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 4.114A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.523A pdb=" N LYS B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing sheet with id= A, first strand: chain 'B' and resid 112 through 116 removed outlier: 4.391A pdb=" N THR B 41 " --> pdb=" O ASP B 116 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1122 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: 2.18 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2462 1.34 - 1.46: 1726 1.46 - 1.58: 3475 1.58 - 1.70: 5 1.70 - 1.82: 66 Bond restraints: 7734 Sorted by residual: bond pdb=" C1' MGT B 201 " pdb=" C2' MGT B 201 " ideal model delta sigma weight residual 1.263 1.523 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C3' MGT B 201 " pdb=" C4' MGT B 201 " ideal model delta sigma weight residual 1.265 1.522 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C2' MGT B 201 " pdb=" C3' MGT B 201 " ideal model delta sigma weight residual 1.652 1.512 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C5 MGT B 201 " pdb=" N7 MGT B 201 " ideal model delta sigma weight residual 1.452 1.324 0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C4 MGT B 201 " pdb=" N3 MGT B 201 " ideal model delta sigma weight residual 1.484 1.359 0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 7729 not shown) Histogram of bond angle deviations from ideal: 96.99 - 105.35: 156 105.35 - 113.71: 4302 113.71 - 122.07: 4767 122.07 - 130.43: 1201 130.43 - 138.79: 48 Bond angle restraints: 10474 Sorted by residual: angle pdb=" C8 MGT B 201 " pdb=" N7 MGT B 201 " pdb=" CM7 MGT B 201 " ideal model delta sigma weight residual 126.79 113.98 12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C1' MGT B 201 " pdb=" N9 MGT B 201 " pdb=" C8 MGT B 201 " ideal model delta sigma weight residual 126.70 115.02 11.68 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C4 MGT B 201 " pdb=" N9 MGT B 201 " pdb=" C8 MGT B 201 " ideal model delta sigma weight residual 106.52 116.82 -10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CA ILE D 856 " pdb=" C ILE D 856 " pdb=" O ILE D 856 " ideal model delta sigma weight residual 121.59 118.20 3.39 1.03e+00 9.43e-01 1.08e+01 angle pdb=" N7 MGT B 201 " pdb=" C8 MGT B 201 " pdb=" N9 MGT B 201 " ideal model delta sigma weight residual 106.68 96.99 9.69 3.00e+00 1.11e-01 1.04e+01 ... (remaining 10469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4163 17.49 - 34.98: 395 34.98 - 52.48: 82 52.48 - 69.97: 16 69.97 - 87.46: 12 Dihedral angle restraints: 4668 sinusoidal: 1946 harmonic: 2722 Sorted by residual: dihedral pdb=" CD ARG B 21 " pdb=" NE ARG B 21 " pdb=" CZ ARG B 21 " pdb=" NH1 ARG B 21 " ideal model delta sinusoidal sigma weight residual 0.00 35.28 -35.28 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA TYR D 859 " pdb=" C TYR D 859 " pdb=" N ARG D 860 " pdb=" CA ARG D 860 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN A 767 " pdb=" CB ASN A 767 " pdb=" CG ASN A 767 " pdb=" OD1 ASN A 767 " ideal model delta sinusoidal sigma weight residual -90.00 -161.10 71.10 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 840 0.040 - 0.079: 231 0.079 - 0.119: 49 0.119 - 0.159: 14 0.159 - 0.198: 4 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CB ILE A 623 " pdb=" CA ILE A 623 " pdb=" CG1 ILE A 623 " pdb=" CG2 ILE A 623 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA ILE D 856 " pdb=" N ILE D 856 " pdb=" C ILE D 856 " pdb=" CB ILE D 856 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" C3' MGT B 201 " pdb=" C2' MGT B 201 " pdb=" C4' MGT B 201 " pdb=" O3' MGT B 201 " both_signs ideal model delta sigma weight residual False -2.43 -2.62 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1135 not shown) Planarity restraints: 1343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 21 " -0.506 9.50e-02 1.11e+02 2.28e-01 3.75e+01 pdb=" NE ARG B 21 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 21 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 21 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 621 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" CG ASN A 621 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 621 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN A 621 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " 0.065 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO A 270 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.053 5.00e-02 4.00e+02 ... (remaining 1340 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 181 2.67 - 3.42: 11556 3.42 - 4.16: 17632 4.16 - 4.90: 33084 Nonbonded interactions: 62459 Sorted by model distance: nonbonded pdb=" NE2 GLN A 599 " pdb=" O GLU B 54 " model vdw 1.191 2.520 nonbonded pdb=" NH2 ARG A 610 " pdb=" O LYS B 67 " model vdw 1.211 2.520 nonbonded pdb=" NE2 HIS A 597 " pdb=" OE1 GLU B 54 " model vdw 1.490 2.520 nonbonded pdb=" CE1 HIS A 597 " pdb=" OE1 GLU B 54 " model vdw 1.675 3.260 nonbonded pdb=" CZ ARG A 610 " pdb=" O LYS B 67 " model vdw 1.802 3.270 ... (remaining 62454 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: 2.340 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: 9.700 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.530 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 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 : 0.007 0.260 7734 Z= 0.464 Angle : 0.726 12.809 10474 Z= 0.365 Chirality : 0.041 0.198 1138 Planarity : 0.008 0.228 1343 Dihedral : 14.586 87.459 2896 Min Nonbonded Distance : 1.191 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.86 % Favored : 96.81 % Rotamer: Outliers : 0.12 % Allowed : 10.72 % Favored : 89.16 % 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: 1.40 (0.30), residues: 910 helix: 1.55 (0.23), residues: 566 sheet: -2.19 (1.02), residues: 23 loop : 0.18 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 416 HIS 0.003 0.001 HIS A 553 PHE 0.028 0.002 PHE A 624 TYR 0.013 0.001 TYR A 169 ARG 0.042 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.7212 (m-30) cc_final: 0.6924 (m-30) REVERT: A 189 ASP cc_start: 0.8222 (p0) cc_final: 0.7508 (p0) REVERT: A 337 VAL cc_start: 0.8358 (t) cc_final: 0.8018 (m) REVERT: A 371 MET cc_start: 0.8376 (tmm) cc_final: 0.7860 (tmm) REVERT: A 372 TYR cc_start: 0.5718 (m-80) cc_final: 0.5296 (m-80) REVERT: B 83 PHE cc_start: 0.7538 (p90) cc_final: 0.7129 (p90) REVERT: B 143 ASP cc_start: 0.7941 (t0) cc_final: 0.7629 (m-30) REVERT: D 870 PHE cc_start: 0.8149 (m-80) cc_final: 0.7699 (m-10) outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.2384 time to fit residues: 80.9194 Evaluate side-chains 137 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 383 GLN A 420 HIS A 649 ASN A 715 GLN A 724 HIS A 759 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7734 Z= 0.230 Angle : 0.671 10.962 10474 Z= 0.333 Chirality : 0.045 0.244 1138 Planarity : 0.005 0.051 1343 Dihedral : 5.580 81.173 1014 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.22 % Allowed : 14.94 % Favored : 80.84 % 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: 1.64 (0.29), residues: 910 helix: 1.75 (0.22), residues: 566 sheet: -1.66 (0.97), residues: 22 loop : 0.22 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 416 HIS 0.006 0.001 HIS A 553 PHE 0.022 0.002 PHE A 624 TYR 0.015 0.002 TYR A 169 ARG 0.006 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.7321 (m-30) cc_final: 0.7001 (m-30) REVERT: A 189 ASP cc_start: 0.8157 (p0) cc_final: 0.7612 (p0) REVERT: A 371 MET cc_start: 0.8533 (tmm) cc_final: 0.7919 (tmm) REVERT: A 435 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (p0) REVERT: B 30 GLU cc_start: 0.8664 (tp30) cc_final: 0.8462 (tp30) REVERT: B 69 ILE cc_start: 0.8108 (mm) cc_final: 0.7553 (tp) REVERT: B 83 PHE cc_start: 0.7289 (p90) cc_final: 0.6453 (p90) REVERT: B 95 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 98 MET cc_start: 0.8387 (mmm) cc_final: 0.8021 (mmm) outliers start: 35 outliers final: 16 residues processed: 171 average time/residue: 0.1979 time to fit residues: 45.8015 Evaluate side-chains 133 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 114 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7734 Z= 0.197 Angle : 0.604 9.175 10474 Z= 0.304 Chirality : 0.042 0.177 1138 Planarity : 0.004 0.034 1343 Dihedral : 5.347 78.283 1014 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 16.75 % Favored : 80.36 % 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: 1.54 (0.28), residues: 910 helix: 1.73 (0.22), residues: 564 sheet: -1.63 (1.15), residues: 16 loop : 0.03 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 416 HIS 0.009 0.001 HIS A 30 PHE 0.014 0.001 PHE A 624 TYR 0.015 0.002 TYR A 169 ARG 0.004 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.7397 (m-30) cc_final: 0.7144 (m-30) REVERT: A 189 ASP cc_start: 0.8277 (p0) cc_final: 0.7605 (p0) REVERT: A 317 ASN cc_start: 0.8832 (m-40) cc_final: 0.8345 (m110) REVERT: A 371 MET cc_start: 0.8494 (tmm) cc_final: 0.7809 (tmm) REVERT: A 568 LYS cc_start: 0.8301 (tttt) cc_final: 0.7978 (tptt) REVERT: B 55 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: B 69 ILE cc_start: 0.8024 (mm) cc_final: 0.7561 (tp) outliers start: 24 outliers final: 17 residues processed: 145 average time/residue: 0.1842 time to fit residues: 36.9249 Evaluate side-chains 124 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 114 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 73 optimal weight: 0.0970 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS A 715 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7734 Z= 0.204 Angle : 0.584 8.933 10474 Z= 0.297 Chirality : 0.042 0.171 1138 Planarity : 0.004 0.036 1343 Dihedral : 5.123 70.427 1014 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.98 % Allowed : 16.27 % Favored : 79.76 % 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: 1.61 (0.28), residues: 910 helix: 1.74 (0.22), residues: 563 sheet: -1.65 (1.11), residues: 16 loop : 0.16 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 416 HIS 0.005 0.001 HIS A 724 PHE 0.016 0.002 PHE A 632 TYR 0.015 0.002 TYR A 169 ARG 0.005 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8362 (p0) cc_final: 0.7747 (p0) REVERT: A 324 SER cc_start: 0.9297 (m) cc_final: 0.8970 (t) REVERT: A 371 MET cc_start: 0.8521 (tmm) cc_final: 0.7799 (tmm) REVERT: B 55 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7664 (pt0) outliers start: 33 outliers final: 17 residues processed: 137 average time/residue: 0.1804 time to fit residues: 34.5744 Evaluate side-chains 120 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 317 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7734 Z= 0.194 Angle : 0.596 9.244 10474 Z= 0.300 Chirality : 0.041 0.162 1138 Planarity : 0.004 0.039 1343 Dihedral : 5.038 65.198 1013 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.34 % Allowed : 17.11 % Favored : 78.55 % 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: 1.47 (0.28), residues: 910 helix: 1.61 (0.21), residues: 571 sheet: -1.64 (1.14), residues: 16 loop : 0.10 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 416 HIS 0.013 0.001 HIS A 30 PHE 0.030 0.001 PHE A 624 TYR 0.014 0.001 TYR D 859 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8870 (mmtm) REVERT: A 189 ASP cc_start: 0.8409 (p0) cc_final: 0.7831 (p0) REVERT: A 279 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8204 (p0) REVERT: A 324 SER cc_start: 0.9322 (m) cc_final: 0.9007 (t) REVERT: A 371 MET cc_start: 0.8499 (tmm) cc_final: 0.7772 (tmm) REVERT: A 592 GLU cc_start: 0.8338 (tp30) cc_final: 0.8074 (tt0) REVERT: A 788 LEU cc_start: 0.8527 (tp) cc_final: 0.8302 (mt) REVERT: B 55 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: B 71 MET cc_start: 0.6857 (mmm) cc_final: 0.6647 (mmm) outliers start: 36 outliers final: 24 residues processed: 135 average time/residue: 0.1975 time to fit residues: 36.7408 Evaluate side-chains 130 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7734 Z= 0.181 Angle : 0.589 8.715 10474 Z= 0.296 Chirality : 0.041 0.195 1138 Planarity : 0.004 0.039 1343 Dihedral : 5.011 60.556 1013 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.25 % Allowed : 17.23 % Favored : 79.52 % 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: 1.49 (0.28), residues: 910 helix: 1.61 (0.22), residues: 574 sheet: -1.71 (1.13), residues: 16 loop : 0.12 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 416 HIS 0.004 0.001 HIS A 367 PHE 0.032 0.002 PHE A 624 TYR 0.015 0.001 TYR D 859 ARG 0.008 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASP cc_start: 0.8451 (p0) cc_final: 0.8209 (p0) REVERT: A 279 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8221 (p0) REVERT: A 324 SER cc_start: 0.9314 (m) cc_final: 0.9036 (t) REVERT: A 371 MET cc_start: 0.8493 (tmm) cc_final: 0.7699 (tmm) REVERT: A 592 GLU cc_start: 0.8331 (tp30) cc_final: 0.8071 (tt0) REVERT: A 788 LEU cc_start: 0.8537 (tp) cc_final: 0.8305 (mt) outliers start: 27 outliers final: 22 residues processed: 140 average time/residue: 0.1944 time to fit residues: 37.1750 Evaluate side-chains 131 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 7734 Z= 0.244 Angle : 0.629 8.635 10474 Z= 0.319 Chirality : 0.043 0.183 1138 Planarity : 0.004 0.040 1343 Dihedral : 4.917 54.151 1013 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.22 % Allowed : 18.31 % Favored : 77.47 % 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: 1.44 (0.28), residues: 910 helix: 1.60 (0.22), residues: 572 sheet: -1.76 (1.10), residues: 16 loop : 0.03 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 416 HIS 0.014 0.001 HIS A 30 PHE 0.015 0.002 PHE A 473 TYR 0.027 0.002 TYR B 138 ARG 0.004 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.8331 (p) cc_final: 0.8011 (m) REVERT: A 188 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8819 (mmtm) REVERT: A 189 ASP cc_start: 0.8772 (p0) cc_final: 0.8288 (p0) REVERT: A 279 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8258 (p0) REVERT: A 284 MET cc_start: 0.7715 (ptp) cc_final: 0.7510 (mtp) REVERT: A 291 MET cc_start: 0.8772 (ppp) cc_final: 0.8140 (ppp) REVERT: A 324 SER cc_start: 0.9324 (m) cc_final: 0.9052 (t) REVERT: A 371 MET cc_start: 0.8491 (tmm) cc_final: 0.7762 (tmm) REVERT: A 372 TYR cc_start: 0.7287 (m-10) cc_final: 0.6791 (m-10) REVERT: A 592 GLU cc_start: 0.8395 (tp30) cc_final: 0.8175 (tt0) REVERT: A 607 LYS cc_start: 0.8359 (tptm) cc_final: 0.7937 (tppt) REVERT: A 720 ILE cc_start: 0.7939 (pt) cc_final: 0.7690 (pt) REVERT: B 55 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: D 858 GLU cc_start: 0.7633 (tp30) cc_final: 0.7340 (pm20) outliers start: 35 outliers final: 27 residues processed: 130 average time/residue: 0.1785 time to fit residues: 32.6568 Evaluate side-chains 129 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.0270 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 ASN A 715 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7734 Z= 0.176 Angle : 0.614 8.553 10474 Z= 0.311 Chirality : 0.042 0.238 1138 Planarity : 0.004 0.040 1343 Dihedral : 4.865 52.697 1013 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.61 % Allowed : 19.40 % Favored : 76.99 % 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: 1.41 (0.28), residues: 910 helix: 1.60 (0.22), residues: 570 sheet: -1.56 (1.14), residues: 16 loop : -0.02 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 416 HIS 0.011 0.001 HIS A 30 PHE 0.015 0.001 PHE A 632 TYR 0.019 0.002 TYR D 859 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.8331 (p) cc_final: 0.8011 (m) REVERT: A 189 ASP cc_start: 0.8792 (p0) cc_final: 0.8340 (p0) REVERT: A 279 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8255 (p0) REVERT: A 324 SER cc_start: 0.9341 (m) cc_final: 0.9095 (t) REVERT: A 371 MET cc_start: 0.8480 (tmm) cc_final: 0.7717 (tmm) REVERT: A 372 TYR cc_start: 0.7319 (m-10) cc_final: 0.6783 (m-10) REVERT: A 607 LYS cc_start: 0.8334 (tptm) cc_final: 0.7850 (tppt) REVERT: A 788 LEU cc_start: 0.8485 (tp) cc_final: 0.8249 (mt) REVERT: B 55 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: B 140 GLN cc_start: 0.8021 (mp10) cc_final: 0.7447 (mm110) REVERT: D 858 GLU cc_start: 0.7613 (tp30) cc_final: 0.7227 (pm20) outliers start: 30 outliers final: 22 residues processed: 132 average time/residue: 0.1902 time to fit residues: 34.4259 Evaluate side-chains 125 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7734 Z= 0.182 Angle : 0.618 9.871 10474 Z= 0.313 Chirality : 0.042 0.274 1138 Planarity : 0.004 0.040 1343 Dihedral : 4.840 50.856 1013 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.49 % Allowed : 20.12 % Favored : 76.39 % 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: 1.34 (0.28), residues: 910 helix: 1.56 (0.22), residues: 569 sheet: -1.63 (1.13), residues: 16 loop : -0.09 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 416 HIS 0.008 0.001 HIS A 30 PHE 0.014 0.001 PHE A 473 TYR 0.018 0.001 TYR D 859 ARG 0.003 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7372 (ptt90) REVERT: A 189 ASP cc_start: 0.8839 (p0) cc_final: 0.8463 (p0) REVERT: A 249 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 256 PHE cc_start: 0.8911 (m-80) cc_final: 0.8480 (m-80) REVERT: A 279 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8266 (p0) REVERT: A 324 SER cc_start: 0.9348 (m) cc_final: 0.9114 (t) REVERT: A 371 MET cc_start: 0.8483 (tmm) cc_final: 0.7628 (tmm) REVERT: A 372 TYR cc_start: 0.7342 (m-10) cc_final: 0.6817 (m-10) REVERT: A 607 LYS cc_start: 0.8355 (tptm) cc_final: 0.7958 (tppt) REVERT: A 788 LEU cc_start: 0.8475 (tp) cc_final: 0.8235 (mt) REVERT: B 55 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: B 140 GLN cc_start: 0.7989 (mp10) cc_final: 0.7374 (mm110) REVERT: D 858 GLU cc_start: 0.7545 (tp30) cc_final: 0.7219 (pm20) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.1911 time to fit residues: 33.8733 Evaluate side-chains 133 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A 715 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 7734 Z= 0.240 Angle : 0.665 13.739 10474 Z= 0.336 Chirality : 0.043 0.273 1138 Planarity : 0.004 0.040 1343 Dihedral : 4.859 47.613 1013 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.73 % Allowed : 20.36 % Favored : 75.90 % 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: 1.30 (0.28), residues: 910 helix: 1.55 (0.22), residues: 566 sheet: -1.86 (1.07), residues: 16 loop : -0.12 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 416 HIS 0.007 0.001 HIS A 30 PHE 0.016 0.002 PHE A 717 TYR 0.017 0.002 TYR D 859 ARG 0.007 0.001 ARG A 716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7452 (ptt90) REVERT: A 189 ASP cc_start: 0.8859 (p0) cc_final: 0.8480 (p0) REVERT: A 213 MET cc_start: 0.5623 (mtp) cc_final: 0.4703 (mtt) REVERT: A 249 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 279 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8291 (p0) REVERT: A 324 SER cc_start: 0.9367 (m) cc_final: 0.9155 (t) REVERT: A 439 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: A 607 LYS cc_start: 0.8426 (tptm) cc_final: 0.8030 (tppt) REVERT: B 55 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: B 140 GLN cc_start: 0.7995 (mp10) cc_final: 0.7452 (tp40) outliers start: 31 outliers final: 23 residues processed: 123 average time/residue: 0.1943 time to fit residues: 33.1583 Evaluate side-chains 122 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain D residue 869 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 439 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.105798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.088523 restraints weight = 24702.919| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.92 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7734 Z= 0.198 Angle : 0.645 9.224 10474 Z= 0.327 Chirality : 0.043 0.262 1138 Planarity : 0.004 0.040 1343 Dihedral : 4.770 46.777 1013 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.37 % Allowed : 20.72 % Favored : 75.90 % 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: 1.33 (0.28), residues: 910 helix: 1.55 (0.22), residues: 572 sheet: -1.68 (1.08), residues: 16 loop : -0.09 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 416 HIS 0.007 0.001 HIS A 30 PHE 0.014 0.002 PHE D 870 TYR 0.053 0.002 TYR B 100 ARG 0.006 0.000 ARG A 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.31 seconds wall clock time: 35 minutes 52.93 seconds (2152.93 seconds total)