Starting phenix.real_space_refine on Fri Mar 15 16:30:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f7a_28899/03_2024/8f7a_28899_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5465 atoms to isotropic. 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 Mg 1 5.21 5 S 38 5.16 5 C 4335 2.51 5 N 1119 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 632": "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: 6742 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5332 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 683, 5327 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 649} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 5431 Chain: "B" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1410 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 169, 'undetermined': 2} Link IDs: {'PTRANS': 6, 'TRANS': 162, None: 2} Not linked: pdbres="PHE B 178 " pdbres=" MG B 301 " Not linked: pdbres=" MG B 301 " pdbres="GTP B 302 " Time building chain proxies: 6.31, per 1000 atoms: 0.94 Number of scatterers: 6742 At special positions: 0 Unit cell: (76.167, 97.092, 104.625, 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 38 16.00 P 3 15.00 Mg 1 11.99 O 1246 8.00 N 1119 7.00 C 4335 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: 2.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 2 sheets defined 64.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 37 through 52 removed outlier: 5.267A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.951A pdb=" N GLY A 57 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 58 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 87 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.871A pdb=" N GLU A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.790A pdb=" N TRP A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.071A pdb=" N MET A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 179 through 198 Proline residue: A 183 - end of helix Proline residue: A 187 - end of helix Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 205 through 228 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 262 through 278 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 287 through 308 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 350 through 367 removed outlier: 3.708A pdb=" N LYS A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Proline residue: A 358 - end of helix removed outlier: 4.156A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 474 through 480 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.138A pdb=" N ARG A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 Processing helix chain 'A' and resid 531 through 551 removed outlier: 3.717A pdb=" N LYS A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 558 through 572 Proline residue: A 562 - end of helix removed outlier: 3.517A pdb=" N LEU A 565 " --> pdb=" O PRO A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 4.402A pdb=" N GLU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 615 removed outlier: 6.028A pdb=" N SER A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 605 " --> pdb=" O MET A 601 " (cutoff:3.500A) Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 620 through 635 removed outlier: 3.677A pdb=" N GLN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 removed outlier: 4.580A pdb=" N GLY A 641 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix removed outlier: 4.885A pdb=" N ILE A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) Proline residue: A 649 - end of helix removed outlier: 3.632A pdb=" N GLN A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 679 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 693 through 703 Processing helix chain 'A' and resid 707 through 722 removed outlier: 4.112A pdb=" N SER A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.343A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 Processing sheet with id= A, first strand: chain 'B' and resid 11 through 16 removed outlier: 3.715A pdb=" N LEU B 15 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 65 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 67 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 48 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.119A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 891 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: 1.77 Time building geometry restraints manager: 3.04 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: 2152 1.34 - 1.46: 1293 1.46 - 1.57: 3379 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6889 Sorted by residual: bond pdb=" CA TRP B 66 " pdb=" CB TRP B 66 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.51e-02 4.39e+03 1.77e+00 bond pdb=" CA THR B 137 " pdb=" CB THR B 137 " ideal model delta sigma weight residual 1.534 1.513 0.021 1.78e-02 3.16e+03 1.36e+00 bond pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA THR A 393 " pdb=" C THR A 393 " ideal model delta sigma weight residual 1.528 1.514 0.014 1.33e-02 5.65e+03 1.07e+00 bond pdb=" CB TRP B 66 " pdb=" CG TRP B 66 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 6884 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.76: 220 106.76 - 113.58: 3974 113.58 - 120.40: 2618 120.40 - 127.22: 2478 127.22 - 134.04: 86 Bond angle restraints: 9376 Sorted by residual: angle pdb=" C THR B 139 " pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 122.09 116.56 5.53 1.79e+00 3.12e-01 9.53e+00 angle pdb=" N ILE A 237 " pdb=" CA ILE A 237 " pdb=" C ILE A 237 " ideal model delta sigma weight residual 109.34 115.13 -5.79 2.08e+00 2.31e-01 7.74e+00 angle pdb=" N LYS B 136 " pdb=" CA LYS B 136 " pdb=" C LYS B 136 " ideal model delta sigma weight residual 113.01 109.68 3.33 1.20e+00 6.94e-01 7.70e+00 angle pdb=" C1' GTP B 302 " pdb=" O4' GTP B 302 " pdb=" C4' GTP B 302 " ideal model delta sigma weight residual 111.80 103.96 7.84 3.00e+00 1.11e-01 6.83e+00 angle pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" N9 GTP B 302 " ideal model delta sigma weight residual 109.47 117.16 -7.69 3.00e+00 1.11e-01 6.57e+00 ... (remaining 9371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3730 17.52 - 35.03: 283 35.03 - 52.55: 93 52.55 - 70.06: 26 70.06 - 87.58: 7 Dihedral angle restraints: 4139 sinusoidal: 1631 harmonic: 2508 Sorted by residual: dihedral pdb=" CA ASN B 158 " pdb=" C ASN B 158 " pdb=" N PHE B 159 " pdb=" CA PHE B 159 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 929 0.055 - 0.110: 160 0.110 - 0.165: 11 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" C1' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" N9 GTP B 302 " pdb=" O4' GTP B 302 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' GTP B 302 " pdb=" C1' GTP B 302 " pdb=" C3' GTP B 302 " pdb=" O2' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" C3' GTP B 302 " pdb=" C2' GTP B 302 " pdb=" C4' GTP B 302 " pdb=" O3' GTP B 302 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1099 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 144 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 145 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 238 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 239 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 682 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 683 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.020 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 2 1.85 - 2.61: 125 2.61 - 3.37: 9963 3.37 - 4.14: 15755 4.14 - 4.90: 29172 Nonbonded interactions: 55017 Sorted by model distance: nonbonded pdb=" OG1 THR B 26 " pdb="MG MG B 301 " model vdw 1.085 2.170 nonbonded pdb="MG MG B 301 " pdb=" O3G GTP B 302 " model vdw 1.776 2.170 nonbonded pdb=" O PHE A 613 " pdb=" OG SER A 617 " model vdw 2.159 2.440 nonbonded pdb=" O PHE A 197 " pdb=" NH1 ARG A 208 " model vdw 2.162 2.520 nonbonded pdb=" OD2 ASP B 93 " pdb=" OG1 THR B 95 " model vdw 2.190 2.440 ... (remaining 55012 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=0.50 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 5.830 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.500 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6889 Z= 0.337 Angle : 0.692 7.842 9376 Z= 0.387 Chirality : 0.041 0.275 1102 Planarity : 0.004 0.042 1177 Dihedral : 15.306 87.575 2501 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 11.80 % Allowed : 9.50 % Favored : 78.70 % 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: -2.21 (0.27), residues: 843 helix: -0.71 (0.21), residues: 545 sheet: -4.45 (0.50), residues: 47 loop : -2.26 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.005 0.001 HIS B 32 PHE 0.014 0.001 PHE B 140 TYR 0.015 0.001 TYR B 148 ARG 0.003 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 223 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8358 (mt0) cc_final: 0.7927 (mt0) REVERT: A 182 MET cc_start: 0.8721 (ttp) cc_final: 0.8476 (ttt) REVERT: A 205 ILE cc_start: 0.8172 (pt) cc_final: 0.7760 (pt) REVERT: A 221 MET cc_start: 0.9070 (ttt) cc_final: 0.8648 (ttt) REVERT: A 279 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6878 (p90) REVERT: A 338 GLU cc_start: 0.7876 (tt0) cc_final: 0.7624 (tp30) REVERT: A 375 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 499 LEU cc_start: 0.9111 (mt) cc_final: 0.8710 (mt) REVERT: A 515 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: A 516 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8190 (mt0) REVERT: A 541 ILE cc_start: 0.8711 (mt) cc_final: 0.8462 (mt) REVERT: A 683 PRO cc_start: 0.8166 (Cg_exo) cc_final: 0.7933 (Cg_endo) REVERT: A 717 LEU cc_start: 0.9214 (mm) cc_final: 0.8954 (mm) REVERT: A 720 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 91 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4141 (ttt) REVERT: B 131 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.3583 (mtm-85) REVERT: B 139 THR cc_start: 0.6653 (t) cc_final: 0.6382 (t) outliers start: 87 outliers final: 20 residues processed: 280 average time/residue: 0.1716 time to fit residues: 63.7094 Evaluate side-chains 174 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.0370 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 242 GLN A 278 ASN A 384 GLN A 414 GLN A 434 GLN A 447 HIS A 515 GLN A 644 GLN A 692 GLN A 712 ASN B 147 GLN B 156 ASN B 175 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6889 Z= 0.202 Angle : 0.718 8.103 9376 Z= 0.361 Chirality : 0.043 0.270 1102 Planarity : 0.005 0.044 1177 Dihedral : 8.638 61.521 961 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 5.83 % Allowed : 21.03 % Favored : 73.13 % 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: -0.81 (0.29), residues: 843 helix: 0.32 (0.22), residues: 541 sheet: -3.68 (0.58), residues: 47 loop : -1.60 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 144 HIS 0.005 0.001 HIS A 341 PHE 0.031 0.002 PHE A 334 TYR 0.011 0.002 TYR A 130 ARG 0.005 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.7881 (pt) cc_final: 0.7652 (pt) REVERT: A 212 VAL cc_start: 0.7930 (t) cc_final: 0.7560 (m) REVERT: A 221 MET cc_start: 0.9012 (ttt) cc_final: 0.8546 (ttt) REVERT: A 279 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6814 (p90) REVERT: A 338 GLU cc_start: 0.8127 (tt0) cc_final: 0.7795 (tp30) REVERT: A 454 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7999 (mm) REVERT: A 720 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: B 87 CYS cc_start: 0.7665 (p) cc_final: 0.7401 (p) REVERT: B 131 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.3240 (mtm-85) REVERT: B 160 GLU cc_start: 0.7066 (pt0) cc_final: 0.6613 (pm20) outliers start: 43 outliers final: 21 residues processed: 194 average time/residue: 0.1490 time to fit residues: 40.8010 Evaluate side-chains 167 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 0.0020 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 76 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN A 640 GLN B 107 HIS B 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6889 Z= 0.195 Angle : 0.685 9.319 9376 Z= 0.340 Chirality : 0.043 0.268 1102 Planarity : 0.004 0.044 1177 Dihedral : 7.135 56.006 941 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.83 % Allowed : 21.57 % Favored : 72.59 % 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: -0.50 (0.29), residues: 843 helix: 0.49 (0.22), residues: 538 sheet: -3.64 (0.56), residues: 46 loop : -1.28 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 144 HIS 0.009 0.001 HIS B 32 PHE 0.012 0.001 PHE B 58 TYR 0.012 0.001 TYR B 100 ARG 0.007 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 158 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.7288 (mtpt) cc_final: 0.6734 (mtpp) REVERT: A 205 ILE cc_start: 0.8030 (pt) cc_final: 0.7590 (pt) REVERT: A 338 GLU cc_start: 0.8495 (tt0) cc_final: 0.7942 (tp30) REVERT: A 454 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8229 (mm) REVERT: A 720 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: B 131 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.3763 (mtm-85) REVERT: B 148 TYR cc_start: 0.8023 (t80) cc_final: 0.6973 (t80) REVERT: B 160 GLU cc_start: 0.7184 (pt0) cc_final: 0.6825 (pm20) outliers start: 43 outliers final: 23 residues processed: 183 average time/residue: 0.1595 time to fit residues: 40.0869 Evaluate side-chains 165 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 475 HIS A 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6889 Z= 0.236 Angle : 0.726 9.114 9376 Z= 0.358 Chirality : 0.044 0.271 1102 Planarity : 0.004 0.040 1177 Dihedral : 6.982 68.469 933 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.70 % Allowed : 22.80 % Favored : 71.51 % 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: -0.49 (0.29), residues: 843 helix: 0.52 (0.23), residues: 532 sheet: -2.88 (0.65), residues: 40 loop : -1.49 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 165 HIS 0.010 0.001 HIS A 475 PHE 0.031 0.002 PHE B 37 TYR 0.012 0.001 TYR B 100 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8980 (pt0) cc_final: 0.8641 (pt0) REVERT: A 172 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 182 MET cc_start: 0.9201 (ttt) cc_final: 0.8873 (ttt) REVERT: A 205 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7954 (pt) REVERT: A 254 ILE cc_start: 0.8582 (mt) cc_final: 0.8209 (pt) REVERT: A 329 PHE cc_start: 0.8096 (t80) cc_final: 0.7813 (t80) REVERT: A 338 GLU cc_start: 0.8689 (tt0) cc_final: 0.8310 (tp30) REVERT: A 454 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 585 GLU cc_start: 0.8680 (tt0) cc_final: 0.8291 (tt0) REVERT: A 628 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 720 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: B 74 PHE cc_start: 0.8090 (m-10) cc_final: 0.7581 (m-80) REVERT: B 147 GLN cc_start: 0.6906 (tp40) cc_final: 0.6621 (tp40) REVERT: B 149 TYR cc_start: 0.8389 (m-10) cc_final: 0.8045 (m-10) REVERT: B 160 GLU cc_start: 0.7489 (pt0) cc_final: 0.7265 (pm20) outliers start: 42 outliers final: 27 residues processed: 169 average time/residue: 0.1581 time to fit residues: 37.0186 Evaluate side-chains 160 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6889 Z= 0.216 Angle : 0.711 11.399 9376 Z= 0.344 Chirality : 0.043 0.187 1102 Planarity : 0.004 0.042 1177 Dihedral : 6.853 74.490 932 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.02 % Allowed : 24.29 % Favored : 70.69 % 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: -0.35 (0.29), residues: 843 helix: 0.56 (0.23), residues: 537 sheet: -2.61 (0.71), residues: 40 loop : -1.36 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 144 HIS 0.007 0.001 HIS B 32 PHE 0.015 0.001 PHE B 37 TYR 0.013 0.001 TYR A 84 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8964 (pt0) cc_final: 0.8549 (pt0) REVERT: A 172 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8355 (mm-30) REVERT: A 193 MET cc_start: 0.9009 (tpp) cc_final: 0.8770 (tpp) REVERT: A 205 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8073 (pt) REVERT: A 213 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 216 THR cc_start: 0.8662 (m) cc_final: 0.8402 (p) REVERT: A 254 ILE cc_start: 0.8653 (mt) cc_final: 0.8305 (pt) REVERT: A 329 PHE cc_start: 0.7933 (t80) cc_final: 0.7629 (t80) REVERT: A 338 GLU cc_start: 0.8717 (tt0) cc_final: 0.8348 (tp30) REVERT: A 429 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 454 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 585 GLU cc_start: 0.8646 (tt0) cc_final: 0.8275 (tt0) REVERT: A 720 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: B 32 HIS cc_start: 0.7847 (m-70) cc_final: 0.7489 (m-70) REVERT: B 67 ASP cc_start: 0.9005 (t0) cc_final: 0.8793 (t0) REVERT: B 74 PHE cc_start: 0.8252 (m-10) cc_final: 0.7938 (m-80) REVERT: B 147 GLN cc_start: 0.6963 (tp40) cc_final: 0.6444 (tp40) outliers start: 37 outliers final: 27 residues processed: 158 average time/residue: 0.1528 time to fit residues: 34.1980 Evaluate side-chains 162 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6889 Z= 0.198 Angle : 0.705 13.131 9376 Z= 0.339 Chirality : 0.043 0.168 1102 Planarity : 0.004 0.040 1177 Dihedral : 6.712 77.854 932 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.02 % Allowed : 24.02 % Favored : 70.96 % 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: -0.21 (0.29), residues: 843 helix: 0.71 (0.23), residues: 530 sheet: -3.01 (0.64), residues: 51 loop : -1.13 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 144 HIS 0.007 0.001 HIS B 32 PHE 0.028 0.001 PHE A 238 TYR 0.008 0.001 TYR B 100 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8440 (mm-30) REVERT: A 213 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 216 THR cc_start: 0.8748 (m) cc_final: 0.8365 (p) REVERT: A 329 PHE cc_start: 0.7893 (t80) cc_final: 0.7598 (t80) REVERT: A 338 GLU cc_start: 0.8768 (tt0) cc_final: 0.8445 (tp30) REVERT: A 429 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 585 GLU cc_start: 0.8708 (tt0) cc_final: 0.8362 (tt0) REVERT: A 720 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 32 HIS cc_start: 0.7875 (m-70) cc_final: 0.7455 (m-70) REVERT: B 74 PHE cc_start: 0.8355 (m-10) cc_final: 0.8055 (m-80) outliers start: 37 outliers final: 28 residues processed: 161 average time/residue: 0.1523 time to fit residues: 34.9415 Evaluate side-chains 152 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 81 optimal weight: 0.0040 chunk 51 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6889 Z= 0.169 Angle : 0.715 14.374 9376 Z= 0.339 Chirality : 0.042 0.164 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.440 79.057 928 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.12 % Allowed : 26.32 % Favored : 70.56 % 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: -0.23 (0.29), residues: 843 helix: 0.74 (0.23), residues: 527 sheet: -2.70 (0.66), residues: 50 loop : -1.30 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 144 HIS 0.008 0.001 HIS A 475 PHE 0.027 0.001 PHE B 37 TYR 0.012 0.001 TYR B 157 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8982 (pt0) cc_final: 0.8537 (pt0) REVERT: A 58 VAL cc_start: 0.8798 (t) cc_final: 0.8376 (t) REVERT: A 172 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 216 THR cc_start: 0.8742 (m) cc_final: 0.8385 (p) REVERT: A 329 PHE cc_start: 0.7738 (t80) cc_final: 0.7392 (t80) REVERT: A 338 GLU cc_start: 0.8747 (tt0) cc_final: 0.8433 (tp30) REVERT: A 429 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 485 ASP cc_start: 0.8618 (m-30) cc_final: 0.8327 (t0) REVERT: A 585 GLU cc_start: 0.8643 (tt0) cc_final: 0.8275 (tt0) REVERT: A 720 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: B 74 PHE cc_start: 0.8295 (m-10) cc_final: 0.8018 (m-80) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 0.1572 time to fit residues: 32.3040 Evaluate side-chains 142 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.0000 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 0.0060 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6889 Z= 0.174 Angle : 0.716 14.504 9376 Z= 0.336 Chirality : 0.042 0.149 1102 Planarity : 0.004 0.041 1177 Dihedral : 6.336 79.622 925 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.93 % Allowed : 24.97 % Favored : 71.10 % 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: -0.13 (0.29), residues: 843 helix: 0.77 (0.23), residues: 527 sheet: -2.64 (0.64), residues: 51 loop : -1.16 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 144 HIS 0.004 0.001 HIS A 341 PHE 0.027 0.001 PHE A 238 TYR 0.012 0.001 TYR B 157 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8994 (pt0) cc_final: 0.8555 (pt0) REVERT: A 182 MET cc_start: 0.9229 (ttt) cc_final: 0.8745 (mtp) REVERT: A 193 MET cc_start: 0.9093 (tpp) cc_final: 0.8615 (tpp) REVERT: A 216 THR cc_start: 0.8779 (m) cc_final: 0.8447 (p) REVERT: A 329 PHE cc_start: 0.7760 (t80) cc_final: 0.7428 (t80) REVERT: A 338 GLU cc_start: 0.8743 (tt0) cc_final: 0.8452 (tp30) REVERT: A 429 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 485 ASP cc_start: 0.8612 (m-30) cc_final: 0.8233 (t0) REVERT: A 488 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 585 GLU cc_start: 0.8696 (tt0) cc_final: 0.8331 (tt0) REVERT: A 720 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: B 32 HIS cc_start: 0.7665 (m-70) cc_final: 0.7344 (m-70) REVERT: B 74 PHE cc_start: 0.8317 (m-10) cc_final: 0.8035 (m-80) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.1568 time to fit residues: 32.7014 Evaluate side-chains 145 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6889 Z= 0.190 Angle : 0.727 14.508 9376 Z= 0.342 Chirality : 0.043 0.214 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.445 80.970 925 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.53 % Allowed : 25.64 % Favored : 70.83 % 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 (0.29), residues: 843 helix: 0.77 (0.23), residues: 528 sheet: -2.59 (0.64), residues: 51 loop : -1.03 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.004 0.001 HIS B 32 PHE 0.028 0.001 PHE B 58 TYR 0.010 0.001 TYR B 100 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9451 (tt) cc_final: 0.9137 (pp) REVERT: A 51 GLU cc_start: 0.8974 (pt0) cc_final: 0.8469 (pt0) REVERT: A 160 LEU cc_start: 0.8609 (tt) cc_final: 0.8264 (mp) REVERT: A 182 MET cc_start: 0.9205 (ttt) cc_final: 0.8724 (mtm) REVERT: A 193 MET cc_start: 0.9160 (tpp) cc_final: 0.8664 (tpp) REVERT: A 216 THR cc_start: 0.8794 (m) cc_final: 0.8453 (p) REVERT: A 329 PHE cc_start: 0.7793 (t80) cc_final: 0.7431 (t80) REVERT: A 338 GLU cc_start: 0.8796 (tt0) cc_final: 0.8546 (tp30) REVERT: A 429 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 585 GLU cc_start: 0.8693 (tt0) cc_final: 0.8277 (tt0) REVERT: A 720 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: B 32 HIS cc_start: 0.7771 (m-70) cc_final: 0.7418 (m-70) REVERT: B 74 PHE cc_start: 0.8404 (m-10) cc_final: 0.8105 (m-80) outliers start: 26 outliers final: 22 residues processed: 139 average time/residue: 0.1491 time to fit residues: 29.2708 Evaluate side-chains 143 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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: 0.7850 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6889 Z= 0.217 Angle : 0.750 15.319 9376 Z= 0.352 Chirality : 0.044 0.217 1102 Planarity : 0.004 0.043 1177 Dihedral : 6.560 80.751 925 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.26 % Allowed : 25.92 % Favored : 70.83 % 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: -0.12 (0.29), residues: 843 helix: 0.74 (0.23), residues: 529 sheet: -2.62 (0.64), residues: 51 loop : -1.07 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 144 HIS 0.005 0.001 HIS A 137 PHE 0.030 0.002 PHE B 58 TYR 0.012 0.001 TYR B 157 ARG 0.002 0.000 ARG A 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9479 (tt) cc_final: 0.9177 (pp) REVERT: A 95 LYS cc_start: 0.8737 (tptt) cc_final: 0.8525 (mtmt) REVERT: A 160 LEU cc_start: 0.8722 (tt) cc_final: 0.8280 (mp) REVERT: A 182 MET cc_start: 0.9197 (ttt) cc_final: 0.8739 (mtm) REVERT: A 193 MET cc_start: 0.9188 (tpp) cc_final: 0.8696 (tpp) REVERT: A 216 THR cc_start: 0.8812 (m) cc_final: 0.8435 (p) REVERT: A 329 PHE cc_start: 0.7886 (t80) cc_final: 0.7542 (t80) REVERT: A 338 GLU cc_start: 0.8786 (tt0) cc_final: 0.8528 (tp30) REVERT: A 429 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 585 GLU cc_start: 0.8727 (tt0) cc_final: 0.8364 (tt0) REVERT: A 628 ASP cc_start: 0.8756 (m-30) cc_final: 0.8255 (t0) REVERT: A 720 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 32 HIS cc_start: 0.7888 (m-70) cc_final: 0.7485 (m-70) REVERT: B 74 PHE cc_start: 0.8545 (m-10) cc_final: 0.8341 (m-80) REVERT: B 147 GLN cc_start: 0.7024 (tp40) cc_final: 0.6392 (tp40) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.1579 time to fit residues: 29.7244 Evaluate side-chains 133 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.0010 chunk 62 optimal weight: 0.0070 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.1940 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.126324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089857 restraints weight = 25272.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.094672 restraints weight = 11764.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098528 restraints weight = 7021.203| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6889 Z= 0.174 Angle : 0.742 14.876 9376 Z= 0.345 Chirality : 0.043 0.203 1102 Planarity : 0.004 0.044 1177 Dihedral : 6.519 81.497 925 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.85 % Allowed : 26.73 % Favored : 70.42 % 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: -0.12 (0.29), residues: 843 helix: 0.72 (0.23), residues: 533 sheet: -2.33 (0.64), residues: 50 loop : -1.13 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 144 HIS 0.005 0.001 HIS A 341 PHE 0.026 0.001 PHE B 58 TYR 0.012 0.001 TYR A 84 ARG 0.004 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.67 seconds wall clock time: 33 minutes 32.17 seconds (2012.17 seconds total)