Starting phenix.real_space_refine on Tue Feb 13 14:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8x_24248/02_2024/7n8x_24248.pdb" } resolution = 3.4 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= 0.023 sd= 0.773 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4202 2.51 5 N 1073 2.21 5 O 1319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 438": "OE1" <-> "OE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 1862": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1093 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Chain: "A" Number of atoms: 5524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5524 Classifications: {'peptide': 691} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 669} Chain breaks: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.61 Number of scatterers: 6617 At special positions: 0 Unit cell: (109.61, 84.75, 91.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1319 8.00 N 1073 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 124 " distance=2.03 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: 2.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 29.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.708A pdb=" N GLU A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.657A pdb=" N GLU A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 4.326A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.616A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.513A pdb=" N ASN A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.334A pdb=" N ALA A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 523 through 539 removed outlier: 4.483A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 588 through 601 removed outlier: 4.026A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 682 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.533A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.741A pdb=" N ILE A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'A' and resid 1773 through 1778 removed outlier: 3.690A pdb=" N ASN A1778 " --> pdb=" O LYS A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1796 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.870A pdb=" N VAL B 30 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 135 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 110 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 65 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629 removed outlier: 4.517A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 649 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 1654 through 1657 removed outlier: 5.879A pdb=" N MET A1655 " --> pdb=" O VAL A1692 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A1765 " --> pdb=" O LEU A1751 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1701 through 1704 removed outlier: 6.043A pdb=" N ILE A1702 " --> pdb=" O ASN A1732 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1844 through 1845 removed outlier: 4.631A pdb=" N TYR A1844 " --> pdb=" O ILE A1853 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2171 1.34 - 1.46: 927 1.46 - 1.57: 3604 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6741 Sorted by residual: bond pdb=" C VAL B 43 " pdb=" O VAL B 43 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.19e-02 7.06e+03 1.84e+00 bond pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" CB PRO A 644 " pdb=" CG PRO A 644 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.45e+00 bond pdb=" C PRO A1847 " pdb=" N PRO A1848 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CG1 ILE A 578 " pdb=" CD1 ILE A 578 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.89: 131 105.89 - 112.91: 3547 112.91 - 119.94: 2349 119.94 - 126.96: 3061 126.96 - 133.99: 50 Bond angle restraints: 9138 Sorted by residual: angle pdb=" C LEU A 519 " pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " ideal model delta sigma weight residual 116.63 111.22 5.41 1.16e+00 7.43e-01 2.18e+01 angle pdb=" CA LEU B 72 " pdb=" CB LEU B 72 " pdb=" CG LEU B 72 " ideal model delta sigma weight residual 116.30 129.98 -13.68 3.50e+00 8.16e-02 1.53e+01 angle pdb=" CG1 ILE A 640 " pdb=" CB ILE A 640 " pdb=" CG2 ILE A 640 " ideal model delta sigma weight residual 110.70 99.57 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" CD PRO A 644 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.23e+01 angle pdb=" C GLU A 613 " pdb=" N ASP A 614 " pdb=" CA ASP A 614 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 ... (remaining 9133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3728 17.27 - 34.54: 316 34.54 - 51.80: 47 51.80 - 69.07: 6 69.07 - 86.34: 8 Dihedral angle restraints: 4105 sinusoidal: 1658 harmonic: 2447 Sorted by residual: dihedral pdb=" CA ARG A 643 " pdb=" C ARG A 643 " pdb=" N PRO A 644 " pdb=" CA PRO A 644 " ideal model delta harmonic sigma weight residual 180.00 -147.82 -32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LYS A1764 " pdb=" C LYS A1764 " pdb=" N ILE A1765 " pdb=" CA ILE A1765 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASP B 104 " pdb=" C ASP B 104 " pdb=" N THR B 105 " pdb=" CA THR B 105 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 4102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 734 0.047 - 0.095: 220 0.095 - 0.142: 72 0.142 - 0.189: 2 0.189 - 0.237: 3 Chirality restraints: 1031 Sorted by residual: chirality pdb=" CB ILE A 640 " pdb=" CA ILE A 640 " pdb=" CG1 ILE A 640 " pdb=" CG2 ILE A 640 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO A 644 " pdb=" N PRO A 644 " pdb=" C PRO A 644 " pdb=" CB PRO A 644 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 1028 not shown) Planarity restraints: 1193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 643 " -0.092 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO A 644 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 699 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C ASN A 699 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 699 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 700 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C VAL A 462 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 463 " 0.011 2.00e-02 2.50e+03 ... (remaining 1190 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 188 2.70 - 3.25: 6969 3.25 - 3.80: 9773 3.80 - 4.35: 12870 4.35 - 4.90: 21155 Nonbonded interactions: 50955 Sorted by model distance: nonbonded pdb=" O ARG A1739 " pdb=" NZ LYS A1764 " model vdw 2.153 2.520 nonbonded pdb=" N GLY A1814 " pdb=" O TYR A1824 " model vdw 2.227 2.520 nonbonded pdb=" OD2 ASP B 89 " pdb=" OH TYR A1819 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP A 423 " pdb=" OG1 THR A 426 " model vdw 2.243 2.440 nonbonded pdb=" O ASN A 699 " pdb=" ND2 ASN A 699 " model vdw 2.269 2.520 ... (remaining 50950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.003 0.060 6741 Z= 0.226 Angle : 0.735 13.681 9138 Z= 0.390 Chirality : 0.049 0.237 1031 Planarity : 0.006 0.139 1193 Dihedral : 13.271 86.339 2522 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.06 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.42 (0.30), residues: 825 helix: 0.74 (0.38), residues: 209 sheet: -1.64 (0.44), residues: 141 loop : -1.52 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 40 HIS 0.009 0.002 HIS B 69 PHE 0.030 0.002 PHE A1676 TYR 0.014 0.001 TYR A1661 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.674 Fit side-chains REVERT: B 108 GLN cc_start: 0.7970 (pm20) cc_final: 0.7311 (pp30) REVERT: A 375 ILE cc_start: 0.6364 (tp) cc_final: 0.5961 (tp) REVERT: A 384 ASN cc_start: 0.5695 (t0) cc_final: 0.5350 (t0) REVERT: A 466 ILE cc_start: 0.8196 (tp) cc_final: 0.7912 (tp) REVERT: A 705 ILE cc_start: 0.7805 (tp) cc_final: 0.7566 (tp) REVERT: A 742 TYR cc_start: 0.7319 (m-80) cc_final: 0.7054 (m-10) REVERT: A 1705 THR cc_start: 0.7932 (m) cc_final: 0.7684 (m) REVERT: A 1727 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6572 (pt0) REVERT: A 1752 MET cc_start: 0.5166 (ttp) cc_final: 0.4879 (ttp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2022 time to fit residues: 39.1027 Evaluate side-chains 128 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6741 Z= 0.194 Angle : 0.656 12.452 9138 Z= 0.332 Chirality : 0.048 0.190 1031 Planarity : 0.005 0.132 1193 Dihedral : 6.030 31.104 894 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Rotamer: Outliers : 1.06 % Allowed : 7.44 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.42 (0.30), residues: 825 helix: 0.74 (0.37), residues: 213 sheet: -1.86 (0.43), residues: 141 loop : -1.46 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 520 HIS 0.003 0.001 HIS B 69 PHE 0.021 0.002 PHE A 780 TYR 0.019 0.002 TYR A1819 ARG 0.002 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.767 Fit side-chains REVERT: B 108 GLN cc_start: 0.7918 (pm20) cc_final: 0.7372 (pp30) REVERT: A 375 ILE cc_start: 0.6533 (tp) cc_final: 0.6209 (mm) REVERT: A 384 ASN cc_start: 0.5727 (t0) cc_final: 0.5125 (t0) REVERT: A 394 TYR cc_start: 0.5426 (m-80) cc_final: 0.4170 (m-10) REVERT: A 410 LEU cc_start: 0.7950 (tp) cc_final: 0.7322 (mp) REVERT: A 466 ILE cc_start: 0.7857 (tp) cc_final: 0.7594 (tp) REVERT: A 569 LEU cc_start: 0.6174 (tp) cc_final: 0.5873 (pp) REVERT: A 705 ILE cc_start: 0.8002 (tp) cc_final: 0.7709 (tp) REVERT: A 766 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7135 (tt0) REVERT: A 818 LYS cc_start: 0.8076 (tptt) cc_final: 0.7491 (tptt) REVERT: A 1727 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6542 (pt0) REVERT: A 1734 ASN cc_start: 0.7682 (m110) cc_final: 0.7155 (p0) REVERT: A 1735 ASP cc_start: 0.6655 (m-30) cc_final: 0.6321 (m-30) REVERT: A 1752 MET cc_start: 0.4954 (ttp) cc_final: 0.4751 (ttp) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.1996 time to fit residues: 37.8493 Evaluate side-chains 133 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 1679 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6741 Z= 0.163 Angle : 0.628 11.291 9138 Z= 0.314 Chirality : 0.047 0.183 1031 Planarity : 0.005 0.129 1193 Dihedral : 5.694 31.330 894 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.33 % Favored : 90.18 % Rotamer: Outliers : 1.46 % Allowed : 10.36 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.29 (0.30), residues: 825 helix: 0.86 (0.37), residues: 214 sheet: -1.95 (0.43), residues: 141 loop : -1.33 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.008 0.001 PHE B 16 TYR 0.016 0.001 TYR A1819 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.751 Fit side-chains REVERT: B 54 LEU cc_start: 0.7742 (mt) cc_final: 0.7347 (tp) REVERT: B 108 GLN cc_start: 0.7901 (pm20) cc_final: 0.7451 (pp30) REVERT: A 375 ILE cc_start: 0.6527 (tp) cc_final: 0.6144 (mm) REVERT: A 384 ASN cc_start: 0.5660 (t0) cc_final: 0.5033 (t0) REVERT: A 394 TYR cc_start: 0.5241 (m-80) cc_final: 0.3873 (m-10) REVERT: A 401 LYS cc_start: 0.6449 (mtmt) cc_final: 0.5488 (mtmt) REVERT: A 410 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7331 (mp) REVERT: A 466 ILE cc_start: 0.7788 (tp) cc_final: 0.7541 (tp) REVERT: A 569 LEU cc_start: 0.6168 (tp) cc_final: 0.5774 (pp) REVERT: A 705 ILE cc_start: 0.7997 (tp) cc_final: 0.7779 (tp) REVERT: A 766 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7063 (tt0) REVERT: A 1708 TYR cc_start: 0.8062 (p90) cc_final: 0.7668 (p90) REVERT: A 1727 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6498 (pt0) REVERT: A 1734 ASN cc_start: 0.7685 (m110) cc_final: 0.7099 (p0) REVERT: A 1752 MET cc_start: 0.5217 (ttp) cc_final: 0.4998 (ttp) outliers start: 11 outliers final: 8 residues processed: 144 average time/residue: 0.1748 time to fit residues: 33.7617 Evaluate side-chains 142 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0050 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.9608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6741 Z= 0.188 Angle : 0.639 10.931 9138 Z= 0.323 Chirality : 0.047 0.189 1031 Planarity : 0.005 0.127 1193 Dihedral : 5.718 31.492 894 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.85 % Favored : 90.67 % Rotamer: Outliers : 2.79 % Allowed : 11.82 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.25 (0.30), residues: 825 helix: 1.06 (0.38), residues: 208 sheet: -1.96 (0.42), residues: 141 loop : -1.35 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.020 0.001 PHE A 780 TYR 0.023 0.002 TYR A 742 ARG 0.002 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.746 Fit side-chains REVERT: B 54 LEU cc_start: 0.8006 (mt) cc_final: 0.7579 (tp) REVERT: B 108 GLN cc_start: 0.7877 (pm20) cc_final: 0.7426 (pp30) REVERT: A 375 ILE cc_start: 0.6672 (tp) cc_final: 0.6251 (tp) REVERT: A 394 TYR cc_start: 0.5517 (m-80) cc_final: 0.3613 (m-80) REVERT: A 404 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: A 410 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7347 (mp) REVERT: A 448 MET cc_start: 0.6284 (mtm) cc_final: 0.5957 (ttp) REVERT: A 466 ILE cc_start: 0.7783 (tp) cc_final: 0.7558 (tp) REVERT: A 569 LEU cc_start: 0.6331 (tp) cc_final: 0.5959 (pp) REVERT: A 705 ILE cc_start: 0.8078 (tp) cc_final: 0.7688 (tp) REVERT: A 709 GLU cc_start: 0.6151 (tt0) cc_final: 0.5664 (tm-30) REVERT: A 766 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7110 (tt0) REVERT: A 818 LYS cc_start: 0.7998 (tptt) cc_final: 0.7436 (tptt) REVERT: A 1727 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6548 (pt0) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.1820 time to fit residues: 35.3127 Evaluate side-chains 151 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1705 THR Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 26 optimal weight: 0.2980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6741 Z= 0.163 Angle : 0.612 10.257 9138 Z= 0.308 Chirality : 0.046 0.188 1031 Planarity : 0.005 0.125 1193 Dihedral : 5.526 31.420 894 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.85 % Favored : 90.67 % Rotamer: Outliers : 2.79 % Allowed : 12.88 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.18 (0.31), residues: 825 helix: 0.93 (0.38), residues: 214 sheet: -1.92 (0.42), residues: 142 loop : -1.23 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 37 HIS 0.002 0.001 HIS B 69 PHE 0.007 0.001 PHE A 701 TYR 0.011 0.001 TYR A1682 ARG 0.001 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.809 Fit side-chains REVERT: B 54 LEU cc_start: 0.8028 (mt) cc_final: 0.7597 (tp) REVERT: B 56 LYS cc_start: 0.8306 (tttt) cc_final: 0.8048 (mttt) REVERT: B 108 GLN cc_start: 0.7879 (pm20) cc_final: 0.7420 (pp30) REVERT: A 375 ILE cc_start: 0.6488 (tp) cc_final: 0.6084 (mm) REVERT: A 384 ASN cc_start: 0.5731 (t0) cc_final: 0.5314 (t0) REVERT: A 394 TYR cc_start: 0.5425 (m-80) cc_final: 0.3456 (m-80) REVERT: A 404 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: A 410 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7309 (mp) REVERT: A 448 MET cc_start: 0.6278 (mtm) cc_final: 0.5922 (ttp) REVERT: A 466 ILE cc_start: 0.7726 (tp) cc_final: 0.7507 (tp) REVERT: A 569 LEU cc_start: 0.6287 (tp) cc_final: 0.5925 (pp) REVERT: A 766 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7117 (tt0) REVERT: A 776 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6345 (tt0) REVERT: A 818 LYS cc_start: 0.8129 (tptt) cc_final: 0.7532 (tptt) REVERT: A 1727 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6540 (pt0) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.1846 time to fit residues: 37.8982 Evaluate side-chains 155 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6741 Z= 0.146 Angle : 0.604 10.056 9138 Z= 0.304 Chirality : 0.046 0.214 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.275 31.413 894 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.61 % Favored : 90.91 % Rotamer: Outliers : 2.92 % Allowed : 14.61 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.02 (0.31), residues: 825 helix: 1.11 (0.38), residues: 208 sheet: -1.72 (0.43), residues: 141 loop : -1.16 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1742 HIS 0.002 0.001 HIS B 69 PHE 0.023 0.001 PHE A 780 TYR 0.021 0.001 TYR A 742 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8262 (tttt) cc_final: 0.8023 (mttt) REVERT: B 108 GLN cc_start: 0.7791 (pm20) cc_final: 0.7466 (pp30) REVERT: B 112 GLU cc_start: 0.7809 (mp0) cc_final: 0.7591 (mp0) REVERT: A 375 ILE cc_start: 0.6371 (tp) cc_final: 0.5942 (mm) REVERT: A 384 ASN cc_start: 0.5669 (t0) cc_final: 0.5280 (t0) REVERT: A 394 TYR cc_start: 0.5061 (m-80) cc_final: 0.3232 (m-80) REVERT: A 410 LEU cc_start: 0.7901 (tp) cc_final: 0.7296 (mp) REVERT: A 448 MET cc_start: 0.6224 (mtm) cc_final: 0.5587 (mpp) REVERT: A 466 ILE cc_start: 0.7651 (tp) cc_final: 0.7436 (tp) REVERT: A 766 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6987 (tt0) REVERT: A 776 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6138 (tt0) REVERT: A 818 LYS cc_start: 0.8126 (tptt) cc_final: 0.7594 (tptt) REVERT: A 1727 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6255 (tp30) REVERT: A 1735 ASP cc_start: 0.6762 (m-30) cc_final: 0.6554 (m-30) outliers start: 22 outliers final: 15 residues processed: 156 average time/residue: 0.1819 time to fit residues: 38.0968 Evaluate side-chains 155 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6741 Z= 0.164 Angle : 0.602 10.224 9138 Z= 0.304 Chirality : 0.046 0.206 1031 Planarity : 0.005 0.123 1193 Dihedral : 5.333 31.530 894 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.85 % Favored : 90.67 % Rotamer: Outliers : 2.92 % Allowed : 15.54 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.04 (0.31), residues: 825 helix: 1.05 (0.38), residues: 208 sheet: -1.78 (0.42), residues: 142 loop : -1.13 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.008 0.001 PHE A 531 TYR 0.013 0.001 TYR A1682 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6458 (mt-10) REVERT: B 54 LEU cc_start: 0.7997 (mt) cc_final: 0.7497 (tp) REVERT: B 56 LYS cc_start: 0.8310 (tttt) cc_final: 0.8051 (mttt) REVERT: B 108 GLN cc_start: 0.7833 (pm20) cc_final: 0.7469 (pp30) REVERT: B 112 GLU cc_start: 0.7857 (mp0) cc_final: 0.7575 (mp0) REVERT: B 130 THR cc_start: 0.8233 (m) cc_final: 0.7983 (p) REVERT: A 375 ILE cc_start: 0.6437 (tp) cc_final: 0.5978 (mm) REVERT: A 384 ASN cc_start: 0.5724 (t0) cc_final: 0.5335 (t0) REVERT: A 394 TYR cc_start: 0.5377 (m-80) cc_final: 0.3308 (m-80) REVERT: A 410 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 448 MET cc_start: 0.6276 (mtm) cc_final: 0.5600 (mpp) REVERT: A 466 ILE cc_start: 0.7678 (tp) cc_final: 0.7457 (tp) REVERT: A 776 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6205 (tt0) REVERT: A 818 LYS cc_start: 0.8183 (tptt) cc_final: 0.7869 (tptt) REVERT: A 1727 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6542 (pt0) outliers start: 22 outliers final: 16 residues processed: 153 average time/residue: 0.1833 time to fit residues: 37.8014 Evaluate side-chains 160 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6741 Z= 0.182 Angle : 0.628 10.240 9138 Z= 0.318 Chirality : 0.047 0.198 1031 Planarity : 0.005 0.122 1193 Dihedral : 5.470 31.366 894 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.09 % Favored : 90.42 % Rotamer: Outliers : 2.92 % Allowed : 16.07 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -1.05 (0.31), residues: 825 helix: 1.07 (0.38), residues: 208 sheet: -1.92 (0.44), residues: 135 loop : -1.12 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.002 0.000 HIS B 69 PHE 0.022 0.001 PHE A 780 TYR 0.013 0.001 TYR A1682 ARG 0.001 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6519 (mt-10) REVERT: B 54 LEU cc_start: 0.8062 (mt) cc_final: 0.7550 (tp) REVERT: B 56 LYS cc_start: 0.8296 (tttt) cc_final: 0.8032 (mttt) REVERT: B 108 GLN cc_start: 0.7874 (pm20) cc_final: 0.7521 (pp30) REVERT: B 112 GLU cc_start: 0.7846 (mp0) cc_final: 0.7592 (mp0) REVERT: A 375 ILE cc_start: 0.6558 (tp) cc_final: 0.6224 (tp) REVERT: A 384 ASN cc_start: 0.5767 (t0) cc_final: 0.5440 (t0) REVERT: A 394 TYR cc_start: 0.5611 (m-80) cc_final: 0.3412 (m-80) REVERT: A 410 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7328 (mp) REVERT: A 448 MET cc_start: 0.6303 (mtm) cc_final: 0.5654 (mpp) REVERT: A 466 ILE cc_start: 0.7726 (tp) cc_final: 0.7506 (tp) REVERT: A 776 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: A 818 LYS cc_start: 0.8194 (tptt) cc_final: 0.7880 (tptt) REVERT: A 1727 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6570 (pt0) REVERT: A 1735 ASP cc_start: 0.6862 (m-30) cc_final: 0.6634 (m-30) outliers start: 22 outliers final: 16 residues processed: 155 average time/residue: 0.1769 time to fit residues: 36.8699 Evaluate side-chains 157 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1734 ASN Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6741 Z= 0.161 Angle : 0.618 10.215 9138 Z= 0.312 Chirality : 0.046 0.175 1031 Planarity : 0.005 0.121 1193 Dihedral : 5.349 31.124 894 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.09 % Favored : 90.42 % Rotamer: Outliers : 2.92 % Allowed : 16.47 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.31), residues: 825 helix: 1.07 (0.38), residues: 208 sheet: -1.82 (0.45), residues: 135 loop : -1.07 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.006 0.001 PHE A 459 TYR 0.013 0.001 TYR A1708 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 54 LEU cc_start: 0.8005 (mt) cc_final: 0.7491 (tp) REVERT: B 56 LYS cc_start: 0.8300 (tttt) cc_final: 0.8041 (mttt) REVERT: B 108 GLN cc_start: 0.7833 (pm20) cc_final: 0.7545 (pp30) REVERT: B 112 GLU cc_start: 0.7822 (mp0) cc_final: 0.7585 (mp0) REVERT: A 375 ILE cc_start: 0.6440 (tp) cc_final: 0.5978 (mm) REVERT: A 384 ASN cc_start: 0.5743 (t0) cc_final: 0.5331 (t0) REVERT: A 394 TYR cc_start: 0.5452 (m-80) cc_final: 0.3209 (m-80) REVERT: A 410 LEU cc_start: 0.7887 (tp) cc_final: 0.7304 (mp) REVERT: A 448 MET cc_start: 0.6290 (mtm) cc_final: 0.5603 (mpp) REVERT: A 466 ILE cc_start: 0.7666 (tp) cc_final: 0.7372 (tp) REVERT: A 516 MET cc_start: 0.5930 (ptm) cc_final: 0.5726 (ptm) REVERT: A 776 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: A 781 ASN cc_start: 0.7520 (t0) cc_final: 0.7296 (t0) REVERT: A 818 LYS cc_start: 0.8200 (tptt) cc_final: 0.7572 (tptt) REVERT: A 1727 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6541 (pt0) REVERT: A 1735 ASP cc_start: 0.6822 (m-30) cc_final: 0.6596 (m-30) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.1777 time to fit residues: 35.6985 Evaluate side-chains 155 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6741 Z= 0.182 Angle : 0.639 10.411 9138 Z= 0.322 Chirality : 0.047 0.151 1031 Planarity : 0.005 0.121 1193 Dihedral : 5.449 31.002 894 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.33 % Favored : 90.18 % Rotamer: Outliers : 2.79 % Allowed : 16.20 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.31), residues: 825 helix: 1.03 (0.38), residues: 208 sheet: -1.89 (0.44), residues: 135 loop : -1.09 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 520 HIS 0.002 0.001 HIS B 69 PHE 0.023 0.001 PHE A 780 TYR 0.031 0.001 TYR A 742 ARG 0.001 0.000 ARG A 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 0.769 Fit side-chains REVERT: B 53 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6498 (mt-10) REVERT: B 54 LEU cc_start: 0.8072 (mt) cc_final: 0.7566 (tp) REVERT: B 56 LYS cc_start: 0.8303 (tttt) cc_final: 0.8049 (mttm) REVERT: B 112 GLU cc_start: 0.7894 (mp0) cc_final: 0.7636 (mp0) REVERT: A 375 ILE cc_start: 0.6516 (tp) cc_final: 0.6207 (tp) REVERT: A 384 ASN cc_start: 0.5627 (t0) cc_final: 0.5313 (t0) REVERT: A 394 TYR cc_start: 0.5571 (m-80) cc_final: 0.3362 (m-80) REVERT: A 404 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: A 410 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7328 (mp) REVERT: A 448 MET cc_start: 0.6326 (mtm) cc_final: 0.5655 (mpp) REVERT: A 466 ILE cc_start: 0.7719 (tp) cc_final: 0.7430 (tp) REVERT: A 776 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: A 818 LYS cc_start: 0.8206 (tptt) cc_final: 0.7830 (tptt) REVERT: A 1727 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6567 (pt0) REVERT: A 1735 ASP cc_start: 0.6847 (m-30) cc_final: 0.6623 (m-30) outliers start: 21 outliers final: 18 residues processed: 143 average time/residue: 0.1920 time to fit residues: 36.6527 Evaluate side-chains 155 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1734 ASN Chi-restraints excluded: chain A residue 1744 ASN Chi-restraints excluded: chain A residue 1763 VAL Chi-restraints excluded: chain A residue 1811 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.209791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.197169 restraints weight = 8667.563| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 1.79 r_work: 0.4289 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6741 Z= 0.164 Angle : 0.621 10.274 9138 Z= 0.312 Chirality : 0.046 0.154 1031 Planarity : 0.005 0.120 1193 Dihedral : 5.367 30.686 894 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.70 % Favored : 89.82 % Rotamer: Outliers : 2.66 % Allowed : 16.73 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -0.97 (0.31), residues: 825 helix: 1.17 (0.38), residues: 202 sheet: -1.79 (0.45), residues: 134 loop : -1.09 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 520 HIS 0.003 0.001 HIS B 69 PHE 0.009 0.001 PHE A 701 TYR 0.030 0.001 TYR A 742 ARG 0.001 0.000 ARG A 643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.91 seconds wall clock time: 34 minutes 16.70 seconds (2056.70 seconds total)