Starting phenix.real_space_refine on Sun Apr 7 03:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/04_2024/7psn_13615_updated.pdb" } resolution = 2.9 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= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6088 2.51 5 N 1604 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B GLU 669": "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: 9464 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.67, per 1000 atoms: 0.60 Number of scatterers: 9464 At special positions: 0 Unit cell: (83.628, 75.348, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 10 15.00 Mg 2 11.99 O 1726 8.00 N 1604 7.00 C 6088 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: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 61.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 105 through 139 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 152 through 200 removed outlier: 3.796A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 211 through 232 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 257 through 303 removed outlier: 3.964A pdb=" N TRP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 314 through 366 Processing helix chain 'A' and resid 372 through 395 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 105 through 139 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 152 through 200 removed outlier: 3.796A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 211 through 232 Processing helix chain 'B' and resid 237 through 252 Processing helix chain 'B' and resid 257 through 303 removed outlier: 3.964A pdb=" N TRP B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 314 through 366 Processing helix chain 'B' and resid 372 through 395 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 539 through 548 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 666 through 675 Processing sheet with id= A, first strand: chain 'A' and resid 457 through 459 Processing sheet with id= B, first strand: chain 'A' and resid 649 through 654 removed outlier: 6.924A pdb=" N VAL A 644 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 653 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 642 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 641 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER A 626 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 467 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 628 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 441 through 443 removed outlier: 7.792A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 457 through 459 Processing sheet with id= E, first strand: chain 'B' and resid 649 through 654 removed outlier: 6.924A pdb=" N VAL B 644 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 653 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 642 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 641 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER B 626 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 467 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR B 628 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 441 through 443 removed outlier: 7.792A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.43: 2478 1.43 - 1.56: 5568 1.56 - 1.68: 14 1.68 - 1.80: 68 Bond restraints: 9636 Sorted by residual: bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.626 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.625 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C6 ANP A 701 " pdb=" N6 ANP A 701 " ideal model delta sigma weight residual 1.340 1.471 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.47: 276 107.47 - 115.33: 5970 115.33 - 123.19: 6411 123.19 - 131.05: 323 131.05 - 138.91: 40 Bond angle restraints: 13020 Sorted by residual: angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.54 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.59 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O3 LOP A 704 " pdb=" P1 LOP A 704 " pdb=" O4 LOP A 704 " ideal model delta sigma weight residual 120.67 109.29 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O3 LOP B 704 " pdb=" P1 LOP B 704 " pdb=" O4 LOP B 704 " ideal model delta sigma weight residual 120.67 109.32 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" O5' ANP A 701 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 5505 25.69 - 51.38: 293 51.38 - 77.07: 44 77.07 - 102.76: 8 102.76 - 128.44: 2 Dihedral angle restraints: 5852 sinusoidal: 2468 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.33 128.44 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.31 128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O2' ANP B 701 " pdb=" C2' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O3' ANP B 701 " ideal model delta sinusoidal sigma weight residual 47.90 -36.39 84.29 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 408 0.072 - 0.108: 114 0.108 - 0.144: 14 0.144 - 0.180: 6 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ANP A 701 " pdb=" C1' ANP A 701 " pdb=" C3' ANP A 701 " pdb=" O2' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ANP B 701 " pdb=" C1' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O2' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C4 LOP A 704 " pdb=" C3 LOP A 704 " pdb=" C5 LOP A 704 " pdb=" O5 LOP A 704 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1493 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP B 703 " 0.204 2.00e-02 2.50e+03 2.05e-01 4.21e+02 pdb=" C14 LOP B 703 " -0.200 2.00e-02 2.50e+03 pdb=" C15 LOP B 703 " -0.210 2.00e-02 2.50e+03 pdb=" C16 LOP B 703 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 703 " -0.204 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C14 LOP A 703 " 0.200 2.00e-02 2.50e+03 pdb=" C15 LOP A 703 " 0.210 2.00e-02 2.50e+03 pdb=" C16 LOP A 703 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 387 " -0.005 2.00e-02 2.50e+03 8.91e-03 7.93e-01 pdb=" C VAL A 387 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 387 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.005 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 70 2.52 - 3.11: 7664 3.11 - 3.71: 14400 3.71 - 4.30: 21027 4.30 - 4.90: 35808 Nonbonded interactions: 78969 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN A 517 " pdb="MG MG A 702 " model vdw 1.923 2.170 nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.963 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.963 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.047 2.170 ... (remaining 78964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=0.98 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: 2.010 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: 7.270 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.990 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.009 0.224 9636 Z= 0.588 Angle : 0.823 13.840 13020 Z= 0.365 Chirality : 0.042 0.180 1496 Planarity : 0.008 0.205 1620 Dihedral : 15.989 128.445 3668 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.21), residues: 1166 helix: -1.13 (0.16), residues: 772 sheet: -3.80 (0.43), residues: 52 loop : -3.49 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 631 PHE 0.009 0.001 PHE A 179 TYR 0.011 0.002 TYR B 161 ARG 0.002 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.000 Fit side-chains REVERT: A 426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.3049 time to fit residues: 170.4589 Evaluate side-chains 74 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 127 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9636 Z= 0.181 Angle : 0.524 7.537 13020 Z= 0.262 Chirality : 0.040 0.148 1496 Planarity : 0.003 0.027 1620 Dihedral : 11.363 115.938 1470 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.80 % Allowed : 11.18 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1166 helix: 0.64 (0.18), residues: 772 sheet: -2.79 (0.48), residues: 62 loop : -2.59 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.002 0.000 HIS B 197 PHE 0.012 0.001 PHE A 391 TYR 0.015 0.001 TYR B 161 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.099 Fit side-chains REVERT: A 331 SER cc_start: 0.7981 (m) cc_final: 0.7764 (m) REVERT: A 421 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7970 (m110) REVERT: A 572 MET cc_start: 0.8527 (mmm) cc_final: 0.8295 (mmm) REVERT: B 331 SER cc_start: 0.7984 (m) cc_final: 0.7768 (m) REVERT: B 421 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7972 (m110) REVERT: B 572 MET cc_start: 0.8532 (mmm) cc_final: 0.8298 (mmm) outliers start: 8 outliers final: 2 residues processed: 127 average time/residue: 1.1880 time to fit residues: 162.5052 Evaluate side-chains 95 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 346 GLN B 304 ASN B 346 GLN B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9636 Z= 0.327 Angle : 0.583 7.412 13020 Z= 0.292 Chirality : 0.043 0.155 1496 Planarity : 0.003 0.033 1620 Dihedral : 10.139 107.035 1470 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.60 % Allowed : 14.97 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1166 helix: 0.81 (0.18), residues: 776 sheet: -2.45 (0.52), residues: 62 loop : -2.18 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 463 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE A 391 TYR 0.013 0.001 TYR B 269 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.112 Fit side-chains REVERT: A 421 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8284 (m110) REVERT: A 632 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7604 (mtt-85) REVERT: B 421 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8285 (m110) REVERT: B 632 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7604 (mtt-85) outliers start: 16 outliers final: 4 residues processed: 144 average time/residue: 1.1862 time to fit residues: 183.8061 Evaluate side-chains 115 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 618 ASN B 134 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9636 Z= 0.285 Angle : 0.539 6.996 13020 Z= 0.273 Chirality : 0.042 0.151 1496 Planarity : 0.003 0.024 1620 Dihedral : 9.745 104.478 1470 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 16.47 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1166 helix: 1.06 (0.18), residues: 776 sheet: -2.14 (0.54), residues: 62 loop : -1.91 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 463 HIS 0.003 0.001 HIS A 197 PHE 0.024 0.001 PHE A 350 TYR 0.026 0.002 TYR A 161 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.115 Fit side-chains REVERT: A 134 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: A 421 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8261 (m110) REVERT: A 581 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6837 (mp) REVERT: B 134 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6767 (mt0) REVERT: B 421 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8258 (m110) REVERT: B 581 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6834 (mp) outliers start: 26 outliers final: 8 residues processed: 127 average time/residue: 1.1662 time to fit residues: 159.7852 Evaluate side-chains 117 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 614 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9636 Z= 0.177 Angle : 0.474 6.615 13020 Z= 0.240 Chirality : 0.039 0.149 1496 Planarity : 0.002 0.024 1620 Dihedral : 9.258 103.507 1470 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.99 % Allowed : 16.17 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1166 helix: 1.48 (0.18), residues: 776 sheet: -2.06 (0.55), residues: 62 loop : -1.73 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS A 197 PHE 0.017 0.001 PHE B 350 TYR 0.018 0.001 TYR B 161 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.148 Fit side-chains REVERT: A 134 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6713 (mt0) REVERT: A 421 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8175 (m110) REVERT: A 581 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6769 (mp) REVERT: A 632 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7508 (mtt-85) REVERT: B 134 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6687 (mt0) REVERT: B 421 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8177 (m110) REVERT: B 632 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7516 (mtt-85) outliers start: 30 outliers final: 5 residues processed: 130 average time/residue: 1.1940 time to fit residues: 167.2055 Evaluate side-chains 116 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9636 Z= 0.363 Angle : 0.571 6.809 13020 Z= 0.287 Chirality : 0.043 0.166 1496 Planarity : 0.003 0.023 1620 Dihedral : 9.577 105.472 1470 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.49 % Allowed : 17.86 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1166 helix: 1.27 (0.18), residues: 776 sheet: -1.89 (0.56), residues: 62 loop : -1.73 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 463 HIS 0.004 0.001 HIS A 197 PHE 0.015 0.001 PHE B 350 TYR 0.029 0.002 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.048 Fit side-chains REVERT: A 134 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6685 (mt0) REVERT: A 421 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8292 (m110) REVERT: A 581 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6883 (mp) REVERT: A 632 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7562 (mtt-85) REVERT: B 134 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: B 421 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8303 (m110) REVERT: B 632 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7570 (mtt-85) outliers start: 35 outliers final: 15 residues processed: 132 average time/residue: 1.0827 time to fit residues: 154.9648 Evaluate side-chains 122 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9636 Z= 0.202 Angle : 0.501 7.227 13020 Z= 0.251 Chirality : 0.040 0.153 1496 Planarity : 0.003 0.024 1620 Dihedral : 9.131 103.524 1470 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.09 % Allowed : 18.56 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1166 helix: 1.55 (0.18), residues: 776 sheet: -1.77 (0.57), residues: 62 loop : -1.56 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS A 197 PHE 0.014 0.001 PHE B 350 TYR 0.033 0.001 TYR B 161 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.072 Fit side-chains REVERT: A 134 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: A 421 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (m110) REVERT: A 572 MET cc_start: 0.8598 (mmm) cc_final: 0.8201 (tpt) REVERT: A 632 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7779 (mtt-85) REVERT: B 134 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6614 (mt0) REVERT: B 350 PHE cc_start: 0.7254 (t80) cc_final: 0.6643 (t80) REVERT: B 421 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8237 (m110) REVERT: B 572 MET cc_start: 0.8598 (mmm) cc_final: 0.8119 (tpt) REVERT: B 632 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7787 (mtt-85) outliers start: 31 outliers final: 9 residues processed: 128 average time/residue: 1.2475 time to fit residues: 172.6037 Evaluate side-chains 113 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 346 GLN B 134 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9636 Z= 0.175 Angle : 0.488 7.748 13020 Z= 0.245 Chirality : 0.039 0.162 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.011 103.626 1470 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.20 % Allowed : 19.36 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1166 helix: 1.73 (0.18), residues: 776 sheet: -1.70 (0.58), residues: 62 loop : -1.54 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.004 0.001 HIS B 235 PHE 0.013 0.001 PHE B 350 TYR 0.029 0.001 TYR B 161 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.744 Fit side-chains REVERT: A 350 PHE cc_start: 0.7140 (t80) cc_final: 0.6543 (t80) REVERT: A 421 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8182 (m110) REVERT: A 632 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7783 (mtt-85) REVERT: B 350 PHE cc_start: 0.7183 (t80) cc_final: 0.6584 (t80) REVERT: B 421 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (m110) REVERT: B 632 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7792 (mtt-85) outliers start: 22 outliers final: 7 residues processed: 123 average time/residue: 1.2080 time to fit residues: 161.7633 Evaluate side-chains 113 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 346 GLN B 134 GLN B 346 GLN B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9636 Z= 0.258 Angle : 0.528 7.827 13020 Z= 0.265 Chirality : 0.041 0.165 1496 Planarity : 0.003 0.024 1620 Dihedral : 9.159 104.496 1470 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.10 % Allowed : 19.46 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1166 helix: 1.61 (0.18), residues: 776 sheet: -1.73 (0.57), residues: 62 loop : -1.60 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 463 HIS 0.003 0.001 HIS B 235 PHE 0.013 0.001 PHE B 350 TYR 0.022 0.001 TYR B 161 ARG 0.006 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.111 Fit side-chains REVERT: A 350 PHE cc_start: 0.7234 (t80) cc_final: 0.6635 (t80) REVERT: A 421 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8250 (m110) REVERT: A 632 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7906 (mtt-85) REVERT: B 350 PHE cc_start: 0.7193 (t80) cc_final: 0.6617 (t80) REVERT: B 421 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (m110) REVERT: B 632 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7941 (mtt-85) outliers start: 21 outliers final: 8 residues processed: 119 average time/residue: 1.2169 time to fit residues: 155.8748 Evaluate side-chains 116 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 618 ASN B 134 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9636 Z= 0.245 Angle : 0.525 7.863 13020 Z= 0.264 Chirality : 0.041 0.163 1496 Planarity : 0.003 0.029 1620 Dihedral : 9.149 104.603 1470 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.50 % Allowed : 20.56 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1166 helix: 1.63 (0.18), residues: 776 sheet: -1.78 (0.56), residues: 62 loop : -1.57 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 463 HIS 0.003 0.001 HIS B 197 PHE 0.013 0.001 PHE B 350 TYR 0.025 0.001 TYR B 161 ARG 0.006 0.000 ARG B 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.067 Fit side-chains REVERT: A 350 PHE cc_start: 0.7230 (t80) cc_final: 0.6602 (t80) REVERT: A 421 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8249 (m110) REVERT: A 572 MET cc_start: 0.8621 (mmm) cc_final: 0.8377 (tpt) REVERT: A 632 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7972 (mtt-85) REVERT: B 350 PHE cc_start: 0.7282 (t80) cc_final: 0.6679 (t80) REVERT: B 421 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8245 (m110) REVERT: B 572 MET cc_start: 0.8624 (mmm) cc_final: 0.8379 (tpt) REVERT: B 632 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7991 (mtt-85) outliers start: 15 outliers final: 8 residues processed: 113 average time/residue: 1.1934 time to fit residues: 145.8829 Evaluate side-chains 113 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 632 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 632 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 346 GLN B 134 GLN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110138 restraints weight = 10911.622| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3220 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9636 Z= 0.197 Angle : 0.500 7.839 13020 Z= 0.252 Chirality : 0.040 0.160 1496 Planarity : 0.003 0.031 1620 Dihedral : 8.954 104.121 1470 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.90 % Allowed : 20.26 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1166 helix: 1.76 (0.18), residues: 778 sheet: -1.85 (0.55), residues: 62 loop : -1.45 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.004 0.001 HIS B 197 PHE 0.012 0.001 PHE B 350 TYR 0.023 0.001 TYR B 161 ARG 0.007 0.000 ARG B 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.74 seconds wall clock time: 60 minutes 49.36 seconds (3649.36 seconds total)