Starting phenix.real_space_refine on Mon Mar 11 04:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s5t_10100/03_2024/6s5t_10100_updated.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 22 5.16 5 C 4429 2.51 5 N 1186 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6958 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5977 Classifications: {'peptide': 752} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PTRANS': 31, 'TRANS': 720} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 950 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.63 Number of scatterers: 6958 At special positions: 0 Unit cell: (101.76, 106.56, 86.4, 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 22 16.00 P 3 15.00 O 1318 8.00 N 1186 7.00 C 4429 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 51.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 185 through 205 Proline residue: A 197 - end of helix removed outlier: 3.794A pdb=" N SER A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.802A pdb=" N GLU A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.566A pdb=" N LYS A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.663A pdb=" N ARG A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.851A pdb=" N ARG A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.589A pdb=" N GLU A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 529 No H-bonds generated for 'chain 'A' and resid 526 through 529' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 564 through 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 588 through 622 removed outlier: 3.644A pdb=" N ARG A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLY A 595 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 596 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 600 " --> pdb=" O TYR A 597 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 601 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 604 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 607 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 613 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 617 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 618 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 653 removed outlier: 3.645A pdb=" N GLU A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.551A pdb=" N THR A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 739 through 773 removed outlier: 3.695A pdb=" N LEU A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 801 through 816 Processing helix chain 'A' and resid 827 through 845 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 30 through 39 removed outlier: 5.737A pdb=" N GLY B 34 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 37 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 139 through 145 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 109 Processing sheet with id= B, first strand: chain 'A' and resid 121 through 124 Processing sheet with id= C, first strand: chain 'A' and resid 131 through 133 removed outlier: 5.833A pdb=" N ALA A 583 " --> pdb=" O LYS A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 291 through 294 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.769A pdb=" N GLY A 406 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS A 444 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 409 through 411 299 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 2.91 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: 2242 1.34 - 1.46: 1722 1.46 - 1.58: 3098 1.58 - 1.70: 5 1.70 - 1.82: 41 Bond restraints: 7108 Sorted by residual: bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.641 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' ANP A 901 " pdb=" PA ANP A 901 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C TYR A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.44e+00 bond pdb=" C LEU A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.18e-02 7.18e+03 5.65e+00 ... (remaining 7103 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.28: 210 107.28 - 114.09: 3725 114.09 - 120.89: 3355 120.89 - 127.70: 2314 127.70 - 134.51: 42 Bond angle restraints: 9646 Sorted by residual: angle pdb=" CA PHE A 269 " pdb=" CB PHE A 269 " pdb=" CG PHE A 269 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" C THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta sigma weight residual 109.02 116.89 -7.87 1.68e+00 3.54e-01 2.19e+01 angle pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " pdb=" CG ASP A 542 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C THR A 451 " pdb=" CA THR A 451 " pdb=" CB THR A 451 " ideal model delta sigma weight residual 110.19 116.95 -6.76 1.62e+00 3.81e-01 1.74e+01 angle pdb=" C ASP A 542 " pdb=" CA ASP A 542 " pdb=" CB ASP A 542 " ideal model delta sigma weight residual 110.42 118.64 -8.22 1.99e+00 2.53e-01 1.71e+01 ... (remaining 9641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 4124 35.54 - 71.08: 154 71.08 - 106.63: 5 106.63 - 142.17: 0 142.17 - 177.71: 1 Dihedral angle restraints: 4284 sinusoidal: 1649 harmonic: 2635 Sorted by residual: dihedral pdb=" O1B ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sinusoidal sigma weight residual 35.15 -142.56 177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA TYR A 222 " pdb=" C TYR A 222 " pdb=" N PRO A 223 " pdb=" CA PRO A 223 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C THR A 654 " pdb=" N THR A 654 " pdb=" CA THR A 654 " pdb=" CB THR A 654 " ideal model delta harmonic sigma weight residual -122.00 -133.28 11.28 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 4281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 681 0.081 - 0.162: 307 0.162 - 0.242: 90 0.242 - 0.323: 11 0.323 - 0.404: 2 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ASN A 271 " pdb=" N ASN A 271 " pdb=" C ASN A 271 " pdb=" CB ASN A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA THR A 654 " pdb=" N THR A 654 " pdb=" C THR A 654 " pdb=" CB THR A 654 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A 542 " pdb=" N ASP A 542 " pdb=" C ASP A 542 " pdb=" CB ASP A 542 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1088 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 606 " -0.013 2.00e-02 2.50e+03 7.66e-03 1.17e+00 pdb=" CG TYR A 606 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 606 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 606 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 606 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 393 " 0.068 9.50e-02 1.11e+02 3.13e-02 1.07e+00 pdb=" NE ARG A 393 " -0.000 2.00e-02 2.50e+03 pdb=" CZ ARG A 393 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 393 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 393 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 242 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 242 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 242 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS A 243 " 0.006 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2648 2.94 - 3.43: 7015 3.43 - 3.92: 11158 3.92 - 4.41: 12126 4.41 - 4.90: 19835 Nonbonded interactions: 52782 Sorted by model distance: nonbonded pdb=" O GLN A 350 " pdb=" OG1 THR A 353 " model vdw 2.450 2.440 nonbonded pdb=" ND2 ASN A 470 " pdb=" O ARG A 536 " model vdw 2.525 2.520 nonbonded pdb=" NE2 GLN A 842 " pdb=" O GLU B 115 " model vdw 2.525 2.520 nonbonded pdb=" O TRP A 845 " pdb=" N GLU A 847 " model vdw 2.525 2.520 nonbonded pdb=" O GLU A 294 " pdb=" OG SER A 297 " model vdw 2.526 2.440 ... (remaining 52777 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.300 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.210 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 0.154 7108 Z= 0.461 Angle : 1.477 10.703 9646 Z= 0.994 Chirality : 0.094 0.404 1091 Planarity : 0.003 0.031 1236 Dihedral : 17.703 177.709 2580 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.06 % Favored : 92.38 % Rotamer: Outliers : 3.93 % Allowed : 13.90 % Favored : 82.16 % Cbeta Deviations : 0.35 % 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: -4.05 (0.22), residues: 892 helix: -2.73 (0.17), residues: 498 sheet: -0.64 (0.92), residues: 32 loop : -2.63 (0.26), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 845 HIS 0.006 0.001 HIS A 800 PHE 0.017 0.002 PHE A 269 TYR 0.015 0.003 TYR A 606 ARG 0.012 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 0.814 Fit side-chains REVERT: A 117 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 218 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8752 (tp30) REVERT: A 239 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 245 TYR cc_start: 0.8840 (m-80) cc_final: 0.8597 (m-10) REVERT: A 282 TYR cc_start: 0.9150 (m-80) cc_final: 0.8789 (m-10) REVERT: A 339 TYR cc_start: 0.7710 (t80) cc_final: 0.7463 (t80) REVERT: A 345 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7677 (mtp85) REVERT: A 381 GLU cc_start: 0.8667 (tp30) cc_final: 0.8349 (tp30) REVERT: A 461 GLU cc_start: 0.8142 (tt0) cc_final: 0.7532 (tm-30) REVERT: A 480 GLU cc_start: 0.8583 (tp30) cc_final: 0.8093 (tm-30) REVERT: A 490 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8698 (pt) REVERT: A 640 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8217 (t0) REVERT: A 682 MET cc_start: 0.9016 (mtt) cc_final: 0.8715 (mtm) REVERT: A 732 TYR cc_start: 0.8997 (t80) cc_final: 0.8729 (t80) REVERT: A 735 GLU cc_start: 0.9302 (pm20) cc_final: 0.8928 (pm20) REVERT: A 771 LYS cc_start: 0.8429 (mttt) cc_final: 0.8006 (mtpp) REVERT: A 817 TYR cc_start: 0.8676 (m-80) cc_final: 0.8471 (m-10) REVERT: A 834 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8747 (ttp-170) REVERT: B 22 LYS cc_start: 0.8635 (mttt) cc_final: 0.7919 (mtmt) REVERT: B 32 GLU cc_start: 0.8675 (pp20) cc_final: 0.7897 (mp0) REVERT: B 68 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 115 GLU cc_start: 0.5243 (mt-10) cc_final: 0.4820 (mt-10) outliers start: 28 outliers final: 8 residues processed: 196 average time/residue: 0.2021 time to fit residues: 51.7221 Evaluate side-chains 140 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 189 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 308 ASN A 517 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7108 Z= 0.221 Angle : 0.564 5.753 9646 Z= 0.297 Chirality : 0.040 0.145 1091 Planarity : 0.004 0.045 1236 Dihedral : 9.268 177.760 1001 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % 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: -1.67 (0.26), residues: 892 helix: -0.55 (0.23), residues: 490 sheet: -0.58 (0.93), residues: 33 loop : -1.86 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 845 HIS 0.003 0.001 HIS A 171 PHE 0.016 0.002 PHE A 475 TYR 0.015 0.001 TYR A 147 ARG 0.004 0.001 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.771 Fit side-chains REVERT: A 114 ASP cc_start: 0.8310 (t0) cc_final: 0.7778 (t0) REVERT: A 218 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8619 (tp30) REVERT: A 232 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7452 (mtm110) REVERT: A 291 MET cc_start: 0.9093 (tmm) cc_final: 0.8847 (tmm) REVERT: A 308 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8622 (m-40) REVERT: A 345 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7652 (mtp85) REVERT: A 414 GLU cc_start: 0.8960 (mp0) cc_final: 0.8606 (mp0) REVERT: A 425 PHE cc_start: 0.8161 (t80) cc_final: 0.7814 (t80) REVERT: A 735 GLU cc_start: 0.9217 (pm20) cc_final: 0.8991 (pm20) REVERT: A 768 GLN cc_start: 0.8779 (tp40) cc_final: 0.8478 (tt0) REVERT: A 771 LYS cc_start: 0.8593 (mttt) cc_final: 0.8097 (mtpt) REVERT: B 22 LYS cc_start: 0.8731 (mttt) cc_final: 0.8027 (mtmt) REVERT: B 32 GLU cc_start: 0.8792 (pp20) cc_final: 0.7860 (mp0) REVERT: B 42 GLN cc_start: 0.8160 (mp10) cc_final: 0.7802 (mp10) REVERT: B 125 MET cc_start: 0.8438 (ttm) cc_final: 0.7920 (ttm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1999 time to fit residues: 44.3287 Evaluate side-chains 124 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 208 HIS A 234 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 280 HIS A 472 HIS A 765 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7108 Z= 0.232 Angle : 0.538 7.136 9646 Z= 0.279 Chirality : 0.040 0.144 1091 Planarity : 0.004 0.046 1236 Dihedral : 8.797 175.956 1001 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 892 helix: 0.22 (0.24), residues: 487 sheet: -0.68 (0.91), residues: 33 loop : -1.70 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 845 HIS 0.003 0.001 HIS A 208 PHE 0.013 0.002 PHE A 292 TYR 0.016 0.001 TYR A 147 ARG 0.005 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8361 (t0) cc_final: 0.7815 (t0) REVERT: A 218 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8687 (tp30) REVERT: A 245 TYR cc_start: 0.8793 (m-80) cc_final: 0.8379 (m-10) REVERT: A 345 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7728 (mtp85) REVERT: A 414 GLU cc_start: 0.8956 (mp0) cc_final: 0.8593 (mp0) REVERT: A 425 PHE cc_start: 0.8188 (t80) cc_final: 0.7817 (t80) REVERT: A 682 MET cc_start: 0.8817 (mtm) cc_final: 0.8581 (mtm) REVERT: A 768 GLN cc_start: 0.8826 (tp40) cc_final: 0.8514 (tt0) REVERT: A 771 LYS cc_start: 0.8657 (mttt) cc_final: 0.8155 (mtpt) REVERT: A 825 TYR cc_start: 0.8951 (m-80) cc_final: 0.8516 (m-10) REVERT: B 22 LYS cc_start: 0.8725 (mttt) cc_final: 0.8075 (mtmt) REVERT: B 32 GLU cc_start: 0.8772 (pp20) cc_final: 0.7916 (mp0) REVERT: B 52 MET cc_start: 0.7436 (mmp) cc_final: 0.7038 (mmp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1826 time to fit residues: 38.0755 Evaluate side-chains 121 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN A 790 GLN A 800 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7108 Z= 0.330 Angle : 0.615 9.593 9646 Z= 0.316 Chirality : 0.042 0.146 1091 Planarity : 0.004 0.052 1236 Dihedral : 9.021 175.456 1001 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -0.78 (0.28), residues: 892 helix: 0.34 (0.25), residues: 487 sheet: -0.46 (0.97), residues: 31 loop : -1.67 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 845 HIS 0.005 0.001 HIS A 280 PHE 0.019 0.002 PHE A 292 TYR 0.022 0.002 TYR A 147 ARG 0.007 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.784 Fit side-chains REVERT: A 114 ASP cc_start: 0.8409 (t0) cc_final: 0.7861 (t0) REVERT: A 245 TYR cc_start: 0.8770 (m-10) cc_final: 0.8539 (m-10) REVERT: A 345 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7734 (mtp85) REVERT: A 414 GLU cc_start: 0.8962 (mp0) cc_final: 0.8487 (mp0) REVERT: A 425 PHE cc_start: 0.8296 (t80) cc_final: 0.7907 (t80) REVERT: A 461 GLU cc_start: 0.8091 (tt0) cc_final: 0.7495 (tm-30) REVERT: A 650 ILE cc_start: 0.9068 (mm) cc_final: 0.8780 (tt) REVERT: A 682 MET cc_start: 0.8830 (mtm) cc_final: 0.8585 (mtm) REVERT: A 768 GLN cc_start: 0.8819 (tp40) cc_final: 0.8460 (tt0) REVERT: A 771 LYS cc_start: 0.8703 (mttt) cc_final: 0.8290 (mtpt) REVERT: A 825 TYR cc_start: 0.9048 (m-80) cc_final: 0.8652 (m-10) REVERT: B 22 LYS cc_start: 0.8685 (mttt) cc_final: 0.8020 (mtmt) REVERT: B 32 GLU cc_start: 0.8790 (pp20) cc_final: 0.7905 (mp0) REVERT: B 106 LEU cc_start: 0.9068 (tp) cc_final: 0.8804 (tt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1820 time to fit residues: 35.1594 Evaluate side-chains 115 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7108 Z= 0.329 Angle : 0.608 10.170 9646 Z= 0.310 Chirality : 0.042 0.141 1091 Planarity : 0.004 0.051 1236 Dihedral : 9.052 173.277 1001 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -0.66 (0.28), residues: 892 helix: 0.42 (0.25), residues: 483 sheet: -0.38 (0.98), residues: 31 loop : -1.56 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 845 HIS 0.004 0.001 HIS A 280 PHE 0.017 0.002 PHE A 292 TYR 0.023 0.002 TYR A 147 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.780 Fit side-chains REVERT: A 114 ASP cc_start: 0.8417 (t0) cc_final: 0.7875 (t0) REVERT: A 245 TYR cc_start: 0.8796 (m-10) cc_final: 0.8536 (m-10) REVERT: A 345 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7722 (mtp85) REVERT: A 414 GLU cc_start: 0.8978 (mp0) cc_final: 0.8494 (mp0) REVERT: A 425 PHE cc_start: 0.8317 (t80) cc_final: 0.7924 (t80) REVERT: A 461 GLU cc_start: 0.8102 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 682 MET cc_start: 0.8844 (mtm) cc_final: 0.8593 (mtm) REVERT: A 768 GLN cc_start: 0.8804 (tp40) cc_final: 0.8450 (tt0) REVERT: A 771 LYS cc_start: 0.8714 (mttt) cc_final: 0.8326 (mtpt) REVERT: A 816 LYS cc_start: 0.8928 (tttp) cc_final: 0.8717 (tttm) REVERT: A 825 TYR cc_start: 0.9051 (m-80) cc_final: 0.8705 (m-10) REVERT: B 22 LYS cc_start: 0.8645 (mttt) cc_final: 0.8023 (mtmt) REVERT: B 32 GLU cc_start: 0.8810 (pp20) cc_final: 0.7926 (mp0) REVERT: B 110 MET cc_start: 0.8003 (mmm) cc_final: 0.7715 (mmp) REVERT: B 112 ASN cc_start: 0.7595 (m-40) cc_final: 0.7239 (m110) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1852 time to fit residues: 36.5939 Evaluate side-chains 119 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN A 458 GLN A 534 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7108 Z= 0.156 Angle : 0.506 7.982 9646 Z= 0.256 Chirality : 0.038 0.137 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.226 170.759 1001 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.14 % Allowed : 1.26 % Favored : 98.60 % 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: -0.31 (0.29), residues: 892 helix: 0.64 (0.25), residues: 485 sheet: -0.55 (0.91), residues: 33 loop : -1.26 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 526 HIS 0.002 0.001 HIS A 472 PHE 0.016 0.001 PHE A 475 TYR 0.014 0.001 TYR A 147 ARG 0.005 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8381 (t0) cc_final: 0.7936 (t0) REVERT: A 345 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7595 (mtp85) REVERT: A 414 GLU cc_start: 0.8948 (mp0) cc_final: 0.8500 (mp0) REVERT: A 425 PHE cc_start: 0.8234 (t80) cc_final: 0.7939 (t80) REVERT: A 590 LYS cc_start: 0.8962 (mttt) cc_final: 0.8565 (mttt) REVERT: A 682 MET cc_start: 0.8781 (mtm) cc_final: 0.8385 (ttm) REVERT: A 768 GLN cc_start: 0.8684 (tp40) cc_final: 0.8383 (tt0) REVERT: A 771 LYS cc_start: 0.8497 (mttt) cc_final: 0.8168 (mtpt) REVERT: A 816 LYS cc_start: 0.8811 (tttp) cc_final: 0.8566 (tttm) REVERT: A 825 TYR cc_start: 0.8809 (m-80) cc_final: 0.8428 (m-10) REVERT: B 32 GLU cc_start: 0.8767 (pp20) cc_final: 0.7970 (mp0) REVERT: B 110 MET cc_start: 0.7870 (mmm) cc_final: 0.7410 (mpp) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1830 time to fit residues: 39.2433 Evaluate side-chains 129 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7108 Z= 0.333 Angle : 0.620 10.436 9646 Z= 0.317 Chirality : 0.042 0.156 1091 Planarity : 0.004 0.050 1236 Dihedral : 8.759 172.614 1001 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.55 (0.28), residues: 892 helix: 0.49 (0.25), residues: 478 sheet: -0.69 (0.92), residues: 33 loop : -1.42 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 845 HIS 0.004 0.001 HIS A 800 PHE 0.017 0.002 PHE A 292 TYR 0.032 0.002 TYR A 147 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7938 (mpt-90) cc_final: 0.7615 (mmm-85) REVERT: A 114 ASP cc_start: 0.8259 (t0) cc_final: 0.7694 (t0) REVERT: A 221 GLU cc_start: 0.8841 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 317 GLU cc_start: 0.8202 (tp30) cc_final: 0.7390 (tm-30) REVERT: A 345 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7738 (mtp85) REVERT: A 414 GLU cc_start: 0.8972 (mp0) cc_final: 0.8478 (mp0) REVERT: A 425 PHE cc_start: 0.8256 (t80) cc_final: 0.7935 (t80) REVERT: A 461 GLU cc_start: 0.8105 (tt0) cc_final: 0.7125 (mp0) REVERT: A 480 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 650 ILE cc_start: 0.9038 (mm) cc_final: 0.8669 (tt) REVERT: A 682 MET cc_start: 0.8816 (mtm) cc_final: 0.8478 (ttm) REVERT: A 768 GLN cc_start: 0.8750 (tp40) cc_final: 0.8420 (tt0) REVERT: A 771 LYS cc_start: 0.8628 (mttt) cc_final: 0.8234 (mtpt) REVERT: A 825 TYR cc_start: 0.8968 (m-80) cc_final: 0.8639 (m-10) REVERT: B 32 GLU cc_start: 0.8798 (pp20) cc_final: 0.7984 (mp0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1906 time to fit residues: 37.1514 Evaluate side-chains 119 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 253 ASN A 517 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7108 Z= 0.194 Angle : 0.534 9.833 9646 Z= 0.270 Chirality : 0.039 0.159 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.407 171.230 1001 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.14 % Allowed : 0.56 % Favored : 99.30 % 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: -0.43 (0.29), residues: 892 helix: 0.54 (0.25), residues: 482 sheet: -0.80 (0.91), residues: 33 loop : -1.29 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 526 HIS 0.002 0.001 HIS A 171 PHE 0.012 0.001 PHE A 829 TYR 0.017 0.001 TYR A 147 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7839 (mpt-90) cc_final: 0.7544 (mmm-85) REVERT: A 194 LEU cc_start: 0.9369 (mm) cc_final: 0.8942 (mm) REVERT: A 253 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8024 (m-40) REVERT: A 345 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7619 (mtp85) REVERT: A 414 GLU cc_start: 0.8925 (mp0) cc_final: 0.8481 (mp0) REVERT: A 425 PHE cc_start: 0.8252 (t80) cc_final: 0.7914 (t80) REVERT: A 480 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 625 MET cc_start: 0.8135 (ttt) cc_final: 0.7465 (ttt) REVERT: A 682 MET cc_start: 0.8756 (mtm) cc_final: 0.8381 (ttm) REVERT: A 768 GLN cc_start: 0.8709 (tp40) cc_final: 0.8411 (tt0) REVERT: A 771 LYS cc_start: 0.8467 (mttt) cc_final: 0.8117 (mtpt) REVERT: A 825 TYR cc_start: 0.8833 (m-80) cc_final: 0.8417 (m-10) REVERT: B 32 GLU cc_start: 0.8778 (pp20) cc_final: 0.8002 (mp0) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1917 time to fit residues: 37.9167 Evaluate side-chains 124 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 75 optimal weight: 0.0980 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 84 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN A 534 ASN A 768 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7108 Z= 0.135 Angle : 0.506 8.760 9646 Z= 0.251 Chirality : 0.037 0.154 1091 Planarity : 0.004 0.055 1236 Dihedral : 7.879 170.084 1001 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.14 % Allowed : 0.42 % Favored : 99.44 % 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: -0.24 (0.29), residues: 892 helix: 0.67 (0.24), residues: 490 sheet: -0.45 (0.95), residues: 33 loop : -1.23 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 635 HIS 0.002 0.000 HIS A 302 PHE 0.012 0.001 PHE A 269 TYR 0.014 0.001 TYR A 443 ARG 0.005 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7701 (mpt-90) cc_final: 0.7445 (mmm-85) REVERT: A 245 TYR cc_start: 0.8743 (m-10) cc_final: 0.7544 (m-10) REVERT: A 317 GLU cc_start: 0.7897 (tp30) cc_final: 0.7039 (tm-30) REVERT: A 345 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7627 (mtp85) REVERT: A 414 GLU cc_start: 0.8921 (mp0) cc_final: 0.8556 (mp0) REVERT: A 425 PHE cc_start: 0.8183 (t80) cc_final: 0.7950 (t80) REVERT: A 480 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 590 LYS cc_start: 0.8944 (mttt) cc_final: 0.8462 (mttt) REVERT: A 625 MET cc_start: 0.8020 (ttt) cc_final: 0.7225 (ttt) REVERT: A 682 MET cc_start: 0.8732 (mtm) cc_final: 0.8270 (ttm) REVERT: A 768 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8440 (tt0) REVERT: A 771 LYS cc_start: 0.8331 (mttt) cc_final: 0.8029 (mtpt) REVERT: A 825 TYR cc_start: 0.8523 (m-80) cc_final: 0.8203 (m-10) REVERT: B 32 GLU cc_start: 0.8722 (pp20) cc_final: 0.7983 (mp0) REVERT: B 110 MET cc_start: 0.7713 (mmm) cc_final: 0.7348 (mpp) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.1926 time to fit residues: 38.9868 Evaluate side-chains 126 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 214 ASN A 308 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7108 Z= 0.185 Angle : 0.534 8.146 9646 Z= 0.266 Chirality : 0.038 0.156 1091 Planarity : 0.004 0.052 1236 Dihedral : 8.015 171.210 1001 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 (0.29), residues: 892 helix: 0.76 (0.25), residues: 483 sheet: 0.30 (0.92), residues: 38 loop : -1.14 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 526 HIS 0.002 0.001 HIS A 171 PHE 0.021 0.001 PHE A 261 TYR 0.014 0.001 TYR A 147 ARG 0.005 0.000 ARG A 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7833 (mpt-90) cc_final: 0.7529 (mmm-85) REVERT: A 317 GLU cc_start: 0.8022 (tp30) cc_final: 0.7090 (tm-30) REVERT: A 345 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7580 (mtp85) REVERT: A 414 GLU cc_start: 0.8916 (mp0) cc_final: 0.8552 (mp0) REVERT: A 425 PHE cc_start: 0.8200 (t80) cc_final: 0.7988 (t80) REVERT: A 590 LYS cc_start: 0.8892 (mttt) cc_final: 0.8476 (mttt) REVERT: A 625 MET cc_start: 0.8048 (ttt) cc_final: 0.7192 (ttt) REVERT: A 682 MET cc_start: 0.8605 (mtm) cc_final: 0.8245 (ttm) REVERT: A 771 LYS cc_start: 0.8362 (mttt) cc_final: 0.8033 (mtpt) REVERT: A 825 TYR cc_start: 0.8585 (m-80) cc_final: 0.8257 (m-10) REVERT: B 3 ASP cc_start: 0.5577 (m-30) cc_final: 0.3945 (m-30) REVERT: B 32 GLU cc_start: 0.8748 (pp20) cc_final: 0.7927 (mp0) REVERT: B 110 MET cc_start: 0.7758 (mmm) cc_final: 0.7415 (mpp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1819 time to fit residues: 37.2385 Evaluate side-chains 127 residues out of total 805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 0.0570 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110525 restraints weight = 10520.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110700 restraints weight = 11471.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112408 restraints weight = 8913.604| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7108 Z= 0.353 Angle : 0.657 10.023 9646 Z= 0.331 Chirality : 0.043 0.160 1091 Planarity : 0.004 0.047 1236 Dihedral : 8.699 172.961 1001 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.40 (0.29), residues: 892 helix: 0.45 (0.24), residues: 491 sheet: -0.30 (0.97), residues: 33 loop : -1.18 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 845 HIS 0.004 0.001 HIS A 280 PHE 0.019 0.002 PHE A 261 TYR 0.020 0.002 TYR A 274 ARG 0.005 0.000 ARG A 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.82 seconds wall clock time: 29 minutes 34.13 seconds (1774.13 seconds total)