Starting phenix.real_space_refine on Sat Mar 16 22:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q0n_18056/03_2024/8q0n_18056_trim_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.124 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 3 5.49 5 S 56 5.16 5 C 5080 2.51 5 N 1360 2.21 5 O 1508 1.98 5 H 7910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15917 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 13084 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 39, 'TRANS': 791} Chain breaks: 2 Chain: "C" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2798 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'04E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'04E:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.61, per 1000 atoms: 0.48 Number of scatterers: 15917 At special positions: 0 Unit cell: (80.898, 92.574, 146.784, 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 56 16.00 P 3 15.00 O 1508 8.00 N 1360 7.00 C 5080 6.00 H 7910 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 5 sheets defined 56.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Proline residue: B 36 - end of helix removed outlier: 4.193A pdb=" N MET B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.594A pdb=" N SER B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.578A pdb=" N VAL B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.577A pdb=" N ASN B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.875A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.821A pdb=" N VAL B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.528A pdb=" N GLN B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 307 Processing helix chain 'B' and resid 313 through 332 removed outlier: 3.565A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 394 removed outlier: 3.599A pdb=" N GLN B 355 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 356 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.545A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B 374 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 390 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 466 removed outlier: 3.542A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 removed outlier: 3.616A pdb=" N PHE B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.556A pdb=" N ILE B 498 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.875A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 538 removed outlier: 3.720A pdb=" N TRP B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 534 " --> pdb=" O TRP B 530 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 594 through 609 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 637 through 654 Processing helix chain 'B' and resid 664 through 671 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 737 through 749 removed outlier: 3.843A pdb=" N GLU B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 766 removed outlier: 3.604A pdb=" N MET B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 removed outlier: 3.668A pdb=" N LEU B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 786 Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 810 through 822 Processing helix chain 'B' and resid 825 through 836 removed outlier: 3.525A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 848 Processing helix chain 'B' and resid 888 through 902 Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 64 through 71 Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 87 through 95 removed outlier: 4.190A pdb=" N ARG C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'C' and resid 165 through 177 removed outlier: 4.072A pdb=" N PHE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 555 through 557 removed outlier: 3.555A pdb=" N ARG B 585 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 557 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 616 through 618 Processing sheet with id= C, first strand: chain 'B' and resid 709 through 714 removed outlier: 3.596A pdb=" N VAL B 710 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 721 " --> pdb=" O VAL B 710 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 859 through 863 Processing sheet with id= E, first strand: chain 'C' and resid 153 through 156 removed outlier: 3.994A pdb=" N LYS C 153 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 2 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 57 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 38 " --> pdb=" O ASP C 57 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 909 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: 5.55 Time building geometry restraints manager: 13.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7882 1.03 - 1.23: 119 1.23 - 1.43: 3302 1.43 - 1.62: 4706 1.62 - 1.82: 83 Bond restraints: 16092 Sorted by residual: bond pdb=" N GLU B 22 " pdb=" CA GLU B 22 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 22 " pdb=" H GLU B 22 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N MET C 1 " pdb=" H MET C 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 04E B1001 " pdb=" O1 04E B1001 " ideal model delta sigma weight residual 1.235 1.259 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 16087 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 334 107.00 - 113.75: 19118 113.75 - 120.50: 5392 120.50 - 127.25: 4153 127.25 - 134.00: 104 Bond angle restraints: 29101 Sorted by residual: angle pdb=" C2' GTP C 201 " pdb=" C3' GTP C 201 " pdb=" C4' GTP C 201 " ideal model delta sigma weight residual 111.00 103.97 7.03 3.00e+00 1.11e-01 5.50e+00 angle pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " pdb=" CG GLN B 774 " ideal model delta sigma weight residual 114.10 118.70 -4.60 2.00e+00 2.50e-01 5.29e+00 angle pdb=" CA MET B 37 " pdb=" CB MET B 37 " pdb=" CG MET B 37 " ideal model delta sigma weight residual 114.10 118.56 -4.46 2.00e+00 2.50e-01 4.96e+00 angle pdb=" N TYR C 72 " pdb=" CA TYR C 72 " pdb=" C TYR C 72 " ideal model delta sigma weight residual 109.81 114.45 -4.64 2.21e+00 2.05e-01 4.41e+00 angle pdb=" C ARG B 655 " pdb=" CA ARG B 655 " pdb=" CB ARG B 655 " ideal model delta sigma weight residual 111.06 107.66 3.40 1.83e+00 2.99e-01 3.45e+00 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 7355 29.79 - 59.59: 227 59.59 - 89.38: 13 89.38 - 119.18: 0 119.18 - 148.97: 2 Dihedral angle restraints: 7597 sinusoidal: 4152 harmonic: 3445 Sorted by residual: dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 -141.76 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -23.95 128.54 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CG LYS B 488 " pdb=" CD LYS B 488 " pdb=" CE LYS B 488 " pdb=" NZ LYS B 488 " ideal model delta sinusoidal sigma weight residual 180.00 121.70 58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 838 0.027 - 0.054: 261 0.054 - 0.081: 92 0.081 - 0.108: 43 0.108 - 0.135: 23 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO B 200 " pdb=" N PRO B 200 " pdb=" C PRO B 200 " pdb=" CB PRO B 200 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE B 860 " pdb=" N ILE B 860 " pdb=" C ILE B 860 " pdb=" CB ILE B 860 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1254 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 68 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 69 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 788 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 789 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 789 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 789 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 33 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 34 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.020 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 994 2.20 - 2.80: 33030 2.80 - 3.40: 43543 3.40 - 4.00: 54567 4.00 - 4.60: 84092 Nonbonded interactions: 216226 Sorted by model distance: nonbonded pdb=" OE1 GLU B 285 " pdb=" H GLU B 285 " model vdw 1.602 1.850 nonbonded pdb=" O LEU B 378 " pdb=" H LYS B 382 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP C 11 " pdb=" HE1 TRP C 97 " model vdw 1.647 1.850 nonbonded pdb=" O MET B 379 " pdb=" H ARG B 383 " model vdw 1.667 1.850 nonbonded pdb=" OD1 ASP C 65 " pdb="HH22 ARG C 68 " model vdw 1.667 1.850 ... (remaining 216221 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: 1.980 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: 0.230 Extract box with map and model: 6.310 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 53.800 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4431 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 : 0.002 0.034 8182 Z= 0.136 Angle : 0.477 7.034 11113 Z= 0.239 Chirality : 0.036 0.135 1257 Planarity : 0.004 0.055 1431 Dihedral : 13.782 148.971 3024 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.28 (0.27), residues: 1001 helix: 1.36 (0.22), residues: 544 sheet: 0.59 (0.76), residues: 50 loop : 0.34 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 97 HIS 0.007 0.001 HIS B 637 PHE 0.015 0.001 PHE C 37 TYR 0.013 0.001 TYR B 313 ARG 0.007 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.4626 (p90) cc_final: 0.4300 (p90) REVERT: B 114 MET cc_start: 0.3889 (mmt) cc_final: 0.3679 (mmt) REVERT: B 312 ASN cc_start: 0.9012 (t0) cc_final: 0.8805 (t0) REVERT: B 634 ASN cc_start: 0.7705 (t0) cc_final: 0.7495 (t0) REVERT: B 718 MET cc_start: 0.5410 (tpp) cc_final: 0.5079 (tpp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3945 time to fit residues: 80.8366 Evaluate side-chains 128 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 173 GLN B 302 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4478 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8182 Z= 0.248 Angle : 0.574 7.868 11113 Z= 0.307 Chirality : 0.039 0.142 1257 Planarity : 0.005 0.057 1431 Dihedral : 7.848 165.381 1094 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.11 % Allowed : 2.46 % Favored : 97.43 % 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: 0.71 (0.26), residues: 1001 helix: 0.80 (0.21), residues: 554 sheet: -0.01 (0.72), residues: 50 loop : 0.26 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 97 HIS 0.008 0.001 HIS B 252 PHE 0.013 0.002 PHE C 78 TYR 0.016 0.002 TYR B 202 ARG 0.016 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7469 (t0) cc_final: 0.7159 (t0) REVERT: B 243 GLU cc_start: 0.2318 (tp30) cc_final: 0.1942 (tp30) REVERT: B 312 ASN cc_start: 0.9122 (t0) cc_final: 0.8844 (t0) REVERT: B 313 TYR cc_start: 0.8042 (p90) cc_final: 0.7719 (p90) REVERT: B 447 MET cc_start: 0.9197 (mmp) cc_final: 0.8942 (mmm) REVERT: B 718 MET cc_start: 0.5367 (tpp) cc_final: 0.5061 (tpp) REVERT: C 166 LYS cc_start: 0.6900 (tptt) cc_final: 0.6648 (ttmm) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.3944 time to fit residues: 79.1005 Evaluate side-chains 119 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 656 GLN C 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4491 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8182 Z= 0.254 Angle : 0.547 7.360 11113 Z= 0.293 Chirality : 0.038 0.148 1257 Planarity : 0.004 0.059 1431 Dihedral : 8.239 178.152 1094 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.11 % Allowed : 1.79 % Favored : 98.10 % 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: 0.34 (0.26), residues: 1001 helix: 0.51 (0.21), residues: 562 sheet: -0.62 (0.74), residues: 48 loop : 0.15 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 364 HIS 0.007 0.001 HIS B 252 PHE 0.029 0.002 PHE B 459 TYR 0.013 0.002 TYR B 202 ARG 0.003 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7564 (t0) cc_final: 0.6896 (p0) REVERT: B 161 ASP cc_start: 0.3812 (m-30) cc_final: 0.3605 (m-30) REVERT: B 312 ASN cc_start: 0.9087 (t0) cc_final: 0.8782 (t0) REVERT: B 313 TYR cc_start: 0.8076 (p90) cc_final: 0.7730 (p90) REVERT: B 447 MET cc_start: 0.9170 (mmp) cc_final: 0.8926 (mmm) REVERT: B 634 ASN cc_start: 0.7794 (t0) cc_final: 0.7588 (t0) REVERT: B 646 GLN cc_start: 0.5327 (mt0) cc_final: 0.5038 (mt0) REVERT: B 718 MET cc_start: 0.5398 (tpp) cc_final: 0.5094 (tpp) REVERT: B 767 PHE cc_start: 0.7135 (m-80) cc_final: 0.6556 (m-10) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.3843 time to fit residues: 73.1901 Evaluate side-chains 111 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8182 Z= 0.259 Angle : 0.551 7.361 11113 Z= 0.295 Chirality : 0.039 0.152 1257 Planarity : 0.005 0.076 1431 Dihedral : 8.322 176.065 1094 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1001 helix: 0.34 (0.21), residues: 571 sheet: -1.29 (0.72), residues: 50 loop : -0.01 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 364 HIS 0.008 0.001 HIS B 252 PHE 0.014 0.002 PHE B 327 TYR 0.014 0.002 TYR B 202 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7597 (t0) cc_final: 0.6937 (p0) REVERT: B 312 ASN cc_start: 0.9061 (t0) cc_final: 0.8763 (t0) REVERT: B 313 TYR cc_start: 0.8129 (p90) cc_final: 0.7728 (p90) REVERT: B 447 MET cc_start: 0.9124 (mmp) cc_final: 0.8895 (mmm) REVERT: B 634 ASN cc_start: 0.7860 (t0) cc_final: 0.7660 (t0) REVERT: B 646 GLN cc_start: 0.5126 (mt0) cc_final: 0.4891 (mt0) REVERT: B 718 MET cc_start: 0.5401 (tpp) cc_final: 0.5100 (tpp) REVERT: B 767 PHE cc_start: 0.7083 (m-80) cc_final: 0.6423 (m-10) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3700 time to fit residues: 72.0775 Evaluate side-chains 113 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4503 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8182 Z= 0.223 Angle : 0.544 7.280 11113 Z= 0.283 Chirality : 0.038 0.141 1257 Planarity : 0.004 0.052 1431 Dihedral : 8.380 171.471 1094 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.18 (0.26), residues: 1001 helix: 0.53 (0.21), residues: 558 sheet: -1.42 (0.72), residues: 50 loop : -0.08 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 56 HIS 0.006 0.001 HIS B 252 PHE 0.013 0.002 PHE B 479 TYR 0.013 0.001 TYR B 288 ARG 0.002 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7618 (t0) cc_final: 0.6900 (p0) REVERT: B 312 ASN cc_start: 0.9027 (t0) cc_final: 0.8743 (t0) REVERT: B 313 TYR cc_start: 0.8146 (p90) cc_final: 0.7700 (p90) REVERT: B 447 MET cc_start: 0.9139 (mmp) cc_final: 0.8893 (mmm) REVERT: B 646 GLN cc_start: 0.5124 (mt0) cc_final: 0.4843 (mt0) REVERT: B 718 MET cc_start: 0.5442 (tpp) cc_final: 0.5136 (tpp) REVERT: B 767 PHE cc_start: 0.7123 (m-80) cc_final: 0.6383 (m-10) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3760 time to fit residues: 69.2323 Evaluate side-chains 105 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4483 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8182 Z= 0.161 Angle : 0.490 6.606 11113 Z= 0.252 Chirality : 0.037 0.137 1257 Planarity : 0.004 0.051 1431 Dihedral : 8.036 168.742 1094 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.52 (0.27), residues: 1001 helix: 0.81 (0.21), residues: 558 sheet: -1.33 (0.73), residues: 50 loop : 0.10 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 693 HIS 0.005 0.001 HIS B 136 PHE 0.013 0.001 PHE B 479 TYR 0.009 0.001 TYR B 202 ARG 0.003 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7565 (t0) cc_final: 0.6810 (p0) REVERT: B 312 ASN cc_start: 0.9012 (t0) cc_final: 0.8729 (t0) REVERT: B 313 TYR cc_start: 0.8153 (p90) cc_final: 0.7696 (p90) REVERT: B 447 MET cc_start: 0.9123 (mmp) cc_final: 0.8860 (mmm) REVERT: B 634 ASN cc_start: 0.7976 (t0) cc_final: 0.7749 (t0) REVERT: B 646 GLN cc_start: 0.5042 (mt0) cc_final: 0.4756 (mt0) REVERT: B 718 MET cc_start: 0.5471 (tpp) cc_final: 0.5165 (tpp) REVERT: B 767 PHE cc_start: 0.7110 (m-80) cc_final: 0.6407 (m-10) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4374 time to fit residues: 76.8914 Evaluate side-chains 108 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4472 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8182 Z= 0.143 Angle : 0.480 6.613 11113 Z= 0.245 Chirality : 0.036 0.136 1257 Planarity : 0.004 0.048 1431 Dihedral : 7.882 167.521 1094 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 0.69 (0.27), residues: 1001 helix: 0.95 (0.22), residues: 558 sheet: -1.17 (0.74), residues: 50 loop : 0.16 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 693 HIS 0.004 0.001 HIS B 637 PHE 0.011 0.001 PHE B 479 TYR 0.007 0.001 TYR B 460 ARG 0.003 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7514 (t0) cc_final: 0.6746 (p0) REVERT: B 312 ASN cc_start: 0.9017 (t0) cc_final: 0.8736 (t0) REVERT: B 313 TYR cc_start: 0.8126 (p90) cc_final: 0.7684 (p90) REVERT: B 447 MET cc_start: 0.9111 (mmp) cc_final: 0.8845 (mmm) REVERT: B 634 ASN cc_start: 0.7935 (t0) cc_final: 0.7707 (t0) REVERT: B 646 GLN cc_start: 0.5025 (mt0) cc_final: 0.4745 (mt0) REVERT: B 718 MET cc_start: 0.5399 (tpp) cc_final: 0.5105 (tpp) REVERT: B 767 PHE cc_start: 0.7103 (m-80) cc_final: 0.6387 (m-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3995 time to fit residues: 70.5796 Evaluate side-chains 111 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN C 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8182 Z= 0.209 Angle : 0.524 7.101 11113 Z= 0.274 Chirality : 0.038 0.140 1257 Planarity : 0.004 0.049 1431 Dihedral : 8.071 165.080 1094 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % 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: 0.42 (0.27), residues: 1001 helix: 0.78 (0.22), residues: 554 sheet: -1.55 (0.71), residues: 50 loop : -0.01 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 56 HIS 0.006 0.001 HIS B 252 PHE 0.020 0.002 PHE B 858 TYR 0.013 0.001 TYR B 288 ARG 0.002 0.000 ARG B 828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7607 (t0) cc_final: 0.6876 (p0) REVERT: B 312 ASN cc_start: 0.9002 (t0) cc_final: 0.8735 (t0) REVERT: B 313 TYR cc_start: 0.8180 (p90) cc_final: 0.7747 (p90) REVERT: B 447 MET cc_start: 0.9120 (mmp) cc_final: 0.8884 (mmm) REVERT: B 634 ASN cc_start: 0.7906 (t0) cc_final: 0.7671 (t0) REVERT: B 646 GLN cc_start: 0.5086 (mt0) cc_final: 0.4830 (mt0) REVERT: B 718 MET cc_start: 0.5427 (tpp) cc_final: 0.5127 (tpp) REVERT: B 767 PHE cc_start: 0.7129 (m-80) cc_final: 0.6411 (m-10) REVERT: B 848 ASN cc_start: 0.5544 (t0) cc_final: 0.5194 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4098 time to fit residues: 72.8650 Evaluate side-chains 108 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4504 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8182 Z= 0.216 Angle : 0.533 7.168 11113 Z= 0.279 Chirality : 0.038 0.142 1257 Planarity : 0.004 0.049 1431 Dihedral : 8.146 165.005 1094 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.25 (0.26), residues: 1001 helix: 0.70 (0.21), residues: 554 sheet: -1.52 (0.62), residues: 61 loop : -0.16 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 56 HIS 0.005 0.001 HIS B 252 PHE 0.013 0.002 PHE B 479 TYR 0.014 0.001 TYR B 288 ARG 0.005 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7634 (t0) cc_final: 0.6950 (p0) REVERT: B 312 ASN cc_start: 0.9017 (t0) cc_final: 0.8796 (t0) REVERT: B 313 TYR cc_start: 0.8237 (p90) cc_final: 0.7908 (p90) REVERT: B 447 MET cc_start: 0.9122 (mmp) cc_final: 0.8893 (mmm) REVERT: B 634 ASN cc_start: 0.7947 (t0) cc_final: 0.7719 (t0) REVERT: B 718 MET cc_start: 0.5377 (tpp) cc_final: 0.5078 (tpp) REVERT: B 767 PHE cc_start: 0.7162 (m-80) cc_final: 0.6528 (m-10) REVERT: B 848 ASN cc_start: 0.5540 (t0) cc_final: 0.5261 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3922 time to fit residues: 72.5013 Evaluate side-chains 107 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN B 646 GLN B 857 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8182 Z= 0.241 Angle : 0.554 7.356 11113 Z= 0.293 Chirality : 0.038 0.143 1257 Planarity : 0.004 0.055 1431 Dihedral : 8.305 166.369 1094 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1001 helix: 0.59 (0.21), residues: 553 sheet: -1.71 (0.60), residues: 61 loop : -0.28 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 796 HIS 0.006 0.001 HIS B 252 PHE 0.014 0.002 PHE B 479 TYR 0.014 0.001 TYR B 288 ARG 0.006 0.001 ARG B 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.7651 (t0) cc_final: 0.7010 (p0) REVERT: B 312 ASN cc_start: 0.9006 (t0) cc_final: 0.8800 (t0) REVERT: B 313 TYR cc_start: 0.8242 (p90) cc_final: 0.7901 (p90) REVERT: B 447 MET cc_start: 0.9127 (mmp) cc_final: 0.8905 (mmm) REVERT: B 634 ASN cc_start: 0.7996 (t0) cc_final: 0.7763 (t0) REVERT: B 718 MET cc_start: 0.5427 (tpp) cc_final: 0.5125 (tpp) REVERT: B 767 PHE cc_start: 0.6999 (m-80) cc_final: 0.6521 (m-10) REVERT: B 848 ASN cc_start: 0.5736 (t0) cc_final: 0.5411 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3939 time to fit residues: 70.0022 Evaluate side-chains 111 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.173505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142756 restraints weight = 36333.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140295 restraints weight = 37657.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143342 restraints weight = 29834.691| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8182 Z= 0.214 Angle : 0.535 7.201 11113 Z= 0.280 Chirality : 0.038 0.141 1257 Planarity : 0.004 0.054 1431 Dihedral : 8.263 166.918 1094 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.13 (0.27), residues: 1001 helix: 0.62 (0.22), residues: 554 sheet: -1.93 (0.68), residues: 49 loop : -0.23 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 693 HIS 0.005 0.001 HIS B 252 PHE 0.013 0.001 PHE B 479 TYR 0.014 0.001 TYR B 288 ARG 0.003 0.000 ARG B 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.52 seconds wall clock time: 64 minutes 20.89 seconds (3860.89 seconds total)