Starting phenix.real_space_refine on Fri Apr 5 21:55:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sd0_40348/04_2024/8sd0_40348_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 34 5.49 5 S 31 5.16 5 C 3598 2.51 5 N 985 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 304": "OE1" <-> "OE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5829 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5140 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 608} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 688 Unusual residues: {'GTP': 1} Classifications: {'RNA': 31, 'undetermined': 1} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 3, 'rna3p': 27, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4208 SG CYS A 810 27.805 58.529 40.084 1.00 67.93 S ATOM 4647 SG CYS A 864 27.991 62.363 40.544 1.00 66.95 S ATOM 4686 SG CYS A 869 27.689 60.503 42.864 1.00 72.48 S Time building chain proxies: 3.65, per 1000 atoms: 0.63 Number of scatterers: 5829 At special positions: 0 Unit cell: (96.6, 81.9, 86.1, 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) Zn 1 29.99 S 31 16.00 P 34 15.00 O 1180 8.00 N 985 7.00 C 3598 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 6 sheets defined 45.8% alpha, 8.0% beta 5 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Proline residue: A 253 - end of helix removed outlier: 3.741A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 434 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.080A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.504A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 601 removed outlier: 4.113A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 removed outlier: 4.306A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 Processing helix chain 'A' and resid 773 through 793 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.365A pdb=" N GLY A 407 " --> pdb=" O ILE A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.648A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 711 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE A 633 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 713 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.754A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= F, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.784A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 2.74 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: 1673 1.34 - 1.46: 1226 1.46 - 1.58: 3002 1.58 - 1.70: 67 1.70 - 1.82: 43 Bond restraints: 6011 Sorted by residual: bond pdb=" C LEU A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.61e+00 bond pdb=" CA PRO A 626 " pdb=" C PRO A 626 " ideal model delta sigma weight residual 1.522 1.545 -0.023 9.80e-03 1.04e+04 5.31e+00 bond pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.00e+00 bond pdb=" CB GLU A 620 " pdb=" CG GLU A 620 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" CB GLU A 581 " pdb=" CG GLU A 581 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 6006 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.49: 56 102.49 - 110.40: 1609 110.40 - 118.31: 3173 118.31 - 126.22: 3276 126.22 - 134.12: 150 Bond angle restraints: 8264 Sorted by residual: angle pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " pdb=" CD GLU A 751 " ideal model delta sigma weight residual 112.60 120.19 -7.59 1.70e+00 3.46e-01 2.00e+01 angle pdb=" N ASP A 392 " pdb=" CA ASP A 392 " pdb=" C ASP A 392 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.93e+01 angle pdb=" CB ARG A 316 " pdb=" CG ARG A 316 " pdb=" CD ARG A 316 " ideal model delta sigma weight residual 111.30 121.01 -9.71 2.30e+00 1.89e-01 1.78e+01 angle pdb=" CA GLU A 751 " pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.62e+01 angle pdb=" C ARG A 559 " pdb=" N MET A 560 " pdb=" CA MET A 560 " ideal model delta sigma weight residual 120.44 125.78 -5.34 1.36e+00 5.41e-01 1.54e+01 ... (remaining 8259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 3164 18.47 - 36.94: 390 36.94 - 55.42: 96 55.42 - 73.89: 52 73.89 - 92.36: 10 Dihedral angle restraints: 3712 sinusoidal: 1837 harmonic: 1875 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 24.12 80.48 1 2.00e+01 2.50e-03 2.00e+01 dihedral pdb=" CA VAL A 877 " pdb=" C VAL A 877 " pdb=" N LYS A 878 " pdb=" CA LYS A 878 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 732 0.050 - 0.100: 170 0.100 - 0.150: 31 0.150 - 0.200: 10 0.200 - 0.250: 3 Chirality restraints: 946 Sorted by residual: chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 943 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 625 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 626 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 778 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" CD GLU A 778 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 778 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 778 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 343 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ILE A 343 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 343 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 344 " 0.017 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1459 2.80 - 3.33: 5409 3.33 - 3.85: 9981 3.85 - 4.38: 10866 4.38 - 4.90: 18318 Nonbonded interactions: 46033 Sorted by model distance: nonbonded pdb=" C3' GTP B 1 " pdb=" OP2 G B 2 " model vdw 2.276 2.776 nonbonded pdb=" O GLU A 583 " pdb=" OG1 THR A 587 " model vdw 2.307 2.440 nonbonded pdb=" O SER A 891 " pdb=" OG SER A 891 " model vdw 2.329 2.440 nonbonded pdb=" CD1 LEU A 611 " pdb=" OH TYR A 715 " model vdw 2.333 3.460 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.352 2.440 ... (remaining 46028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 1.830 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.067 6011 Z= 0.258 Angle : 0.860 11.624 8264 Z= 0.451 Chirality : 0.047 0.250 946 Planarity : 0.007 0.094 936 Dihedral : 18.359 92.360 2490 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.52 % Allowed : 24.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.31), residues: 628 helix: 0.17 (0.29), residues: 283 sheet: -2.01 (0.53), residues: 86 loop : -2.12 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 646 HIS 0.002 0.001 HIS A 782 PHE 0.026 0.002 PHE A 776 TYR 0.036 0.002 TYR A 548 ARG 0.023 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.650 Fit side-chains REVERT: A 317 HIS cc_start: 0.6894 (m-70) cc_final: 0.5916 (m-70) REVERT: A 503 GLU cc_start: 0.7620 (pm20) cc_final: 0.6557 (pm20) REVERT: A 876 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.6992 (t70) REVERT: A 895 GLU cc_start: 0.7731 (pt0) cc_final: 0.7286 (pt0) outliers start: 3 outliers final: 1 residues processed: 109 average time/residue: 0.1933 time to fit residues: 27.5867 Evaluate side-chains 90 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 341 ASN A 500 GLN A 623 HIS A 710 ASN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6011 Z= 0.155 Angle : 0.524 7.749 8264 Z= 0.262 Chirality : 0.037 0.149 946 Planarity : 0.004 0.046 936 Dihedral : 15.523 93.925 1178 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.17 % Allowed : 24.87 % 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: -0.80 (0.34), residues: 628 helix: 1.24 (0.31), residues: 288 sheet: -2.03 (0.53), residues: 86 loop : -2.10 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 646 HIS 0.009 0.001 HIS A 623 PHE 0.020 0.001 PHE A 616 TYR 0.027 0.001 TYR A 548 ARG 0.007 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8546 (tpp80) cc_final: 0.7972 (tpp-160) REVERT: A 876 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.6831 (t70) REVERT: A 895 GLU cc_start: 0.7697 (pt0) cc_final: 0.7276 (pt0) outliers start: 24 outliers final: 11 residues processed: 110 average time/residue: 0.1702 time to fit residues: 25.2245 Evaluate side-chains 94 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 341 ASN A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6011 Z= 0.122 Angle : 0.506 7.637 8264 Z= 0.253 Chirality : 0.037 0.128 946 Planarity : 0.003 0.041 936 Dihedral : 15.469 93.308 1178 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.65 % Allowed : 25.57 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.34), residues: 628 helix: 1.49 (0.31), residues: 293 sheet: -1.85 (0.55), residues: 83 loop : -2.02 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 646 HIS 0.002 0.000 HIS A 280 PHE 0.029 0.001 PHE A 616 TYR 0.024 0.001 TYR A 548 ARG 0.004 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6863 (mmm160) cc_final: 0.6513 (mmm160) REVERT: A 623 HIS cc_start: 0.8426 (t-90) cc_final: 0.8164 (t-170) REVERT: A 876 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6798 (t70) REVERT: A 895 GLU cc_start: 0.7692 (pt0) cc_final: 0.7248 (pt0) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.1588 time to fit residues: 24.8378 Evaluate side-chains 101 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6011 Z= 0.273 Angle : 0.600 9.086 8264 Z= 0.296 Chirality : 0.040 0.186 946 Planarity : 0.004 0.043 936 Dihedral : 15.406 91.183 1178 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.22 % Allowed : 25.22 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.35), residues: 628 helix: 1.66 (0.32), residues: 292 sheet: -2.09 (0.54), residues: 83 loop : -1.98 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 646 HIS 0.004 0.001 HIS A 871 PHE 0.030 0.002 PHE A 616 TYR 0.026 0.002 TYR A 548 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9180 (mmm) cc_final: 0.8597 (mmm) REVERT: A 623 HIS cc_start: 0.8557 (t-90) cc_final: 0.8346 (t-170) REVERT: A 777 ARG cc_start: 0.8630 (tpp80) cc_final: 0.7962 (tpp-160) REVERT: A 876 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6674 (t70) outliers start: 30 outliers final: 21 residues processed: 118 average time/residue: 0.1602 time to fit residues: 25.7517 Evaluate side-chains 110 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 500 GLN A 868 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.185 Angle : 0.561 8.334 8264 Z= 0.278 Chirality : 0.039 0.180 946 Planarity : 0.003 0.044 936 Dihedral : 15.451 91.544 1178 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.39 % Allowed : 25.74 % Favored : 68.87 % 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 (0.35), residues: 628 helix: 1.68 (0.31), residues: 294 sheet: -2.05 (0.54), residues: 83 loop : -1.95 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.029 0.001 PHE A 616 TYR 0.026 0.001 TYR A 548 ARG 0.007 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.7185 (mmm160) cc_final: 0.6848 (mmm160) REVERT: A 387 MET cc_start: 0.9169 (mmm) cc_final: 0.8580 (mmm) REVERT: A 460 PHE cc_start: 0.7805 (m-10) cc_final: 0.7587 (m-10) REVERT: A 777 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8006 (tpp-160) REVERT: A 876 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.6746 (t70) outliers start: 31 outliers final: 26 residues processed: 116 average time/residue: 0.1624 time to fit residues: 25.5271 Evaluate side-chains 117 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6011 Z= 0.248 Angle : 0.599 8.734 8264 Z= 0.300 Chirality : 0.040 0.173 946 Planarity : 0.003 0.044 936 Dihedral : 15.456 90.734 1178 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 6.09 % Allowed : 25.57 % Favored : 68.35 % 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: -0.41 (0.35), residues: 628 helix: 1.62 (0.32), residues: 293 sheet: -2.07 (0.54), residues: 83 loop : -1.97 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 646 HIS 0.005 0.001 HIS A 623 PHE 0.038 0.002 PHE A 616 TYR 0.031 0.002 TYR A 548 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6962 (mmm160) REVERT: A 363 LEU cc_start: 0.8802 (tp) cc_final: 0.8568 (tp) REVERT: A 387 MET cc_start: 0.9225 (mmm) cc_final: 0.8645 (mmm) REVERT: A 538 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 777 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8003 (tpp-160) REVERT: A 876 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.6758 (t70) outliers start: 35 outliers final: 27 residues processed: 122 average time/residue: 0.1638 time to fit residues: 27.3052 Evaluate side-chains 121 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.202 Angle : 0.598 10.592 8264 Z= 0.295 Chirality : 0.039 0.167 946 Planarity : 0.003 0.044 936 Dihedral : 15.499 90.629 1178 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.57 % Allowed : 26.78 % Favored : 67.65 % 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: -0.38 (0.35), residues: 628 helix: 1.61 (0.31), residues: 293 sheet: -2.03 (0.54), residues: 83 loop : -1.92 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 646 HIS 0.003 0.001 HIS A 871 PHE 0.016 0.001 PHE A 616 TYR 0.031 0.001 TYR A 548 ARG 0.003 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6977 (mmm160) REVERT: A 363 LEU cc_start: 0.8796 (tp) cc_final: 0.8565 (tp) REVERT: A 387 MET cc_start: 0.9225 (mmm) cc_final: 0.8642 (mmm) REVERT: A 777 ARG cc_start: 0.8650 (tpp80) cc_final: 0.8079 (tpp-160) REVERT: A 876 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6776 (t70) REVERT: A 895 GLU cc_start: 0.7851 (pt0) cc_final: 0.7288 (pt0) outliers start: 32 outliers final: 29 residues processed: 122 average time/residue: 0.1608 time to fit residues: 26.8284 Evaluate side-chains 121 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6011 Z= 0.286 Angle : 0.658 10.640 8264 Z= 0.326 Chirality : 0.041 0.179 946 Planarity : 0.004 0.045 936 Dihedral : 15.493 89.976 1178 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 6.26 % Allowed : 25.91 % Favored : 67.83 % 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: -0.44 (0.35), residues: 628 helix: 1.67 (0.32), residues: 283 sheet: -2.15 (0.56), residues: 81 loop : -1.91 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 646 HIS 0.006 0.001 HIS A 280 PHE 0.017 0.002 PHE A 616 TYR 0.036 0.002 TYR A 548 ARG 0.004 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8854 (tp) cc_final: 0.8629 (tp) REVERT: A 387 MET cc_start: 0.9268 (mmm) cc_final: 0.8683 (mmm) REVERT: A 876 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.6695 (t70) outliers start: 36 outliers final: 30 residues processed: 120 average time/residue: 0.1541 time to fit residues: 25.3958 Evaluate side-chains 121 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 910 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.196 Angle : 0.630 11.020 8264 Z= 0.311 Chirality : 0.040 0.175 946 Planarity : 0.004 0.045 936 Dihedral : 15.556 90.203 1178 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.57 % Allowed : 26.43 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.35), residues: 628 helix: 1.55 (0.32), residues: 293 sheet: -1.99 (0.55), residues: 83 loop : -1.90 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 646 HIS 0.003 0.001 HIS A 280 PHE 0.016 0.001 PHE A 616 TYR 0.035 0.001 TYR A 548 ARG 0.009 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ASN cc_start: 0.8354 (m110) cc_final: 0.8081 (m110) REVERT: A 876 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6793 (t70) REVERT: A 895 GLU cc_start: 0.7842 (pt0) cc_final: 0.7289 (pt0) outliers start: 32 outliers final: 28 residues processed: 123 average time/residue: 0.1664 time to fit residues: 27.4007 Evaluate side-chains 121 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 41 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 500 GLN A 784 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6011 Z= 0.153 Angle : 0.613 11.248 8264 Z= 0.303 Chirality : 0.040 0.190 946 Planarity : 0.004 0.045 936 Dihedral : 15.615 89.922 1178 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.00 % Allowed : 27.83 % Favored : 68.17 % 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: -0.33 (0.35), residues: 628 helix: 1.55 (0.32), residues: 294 sheet: -1.80 (0.56), residues: 83 loop : -1.84 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 646 HIS 0.001 0.000 HIS A 375 PHE 0.015 0.001 PHE A 776 TYR 0.034 0.001 TYR A 548 ARG 0.009 0.000 ARG A 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9146 (mmp) cc_final: 0.8726 (mmm) REVERT: A 460 PHE cc_start: 0.7822 (m-10) cc_final: 0.7309 (m-10) REVERT: A 573 ASN cc_start: 0.8391 (m110) cc_final: 0.8136 (m110) REVERT: A 591 GLU cc_start: 0.8383 (pt0) cc_final: 0.8173 (pt0) REVERT: A 876 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.6815 (t70) REVERT: A 895 GLU cc_start: 0.7798 (pt0) cc_final: 0.7325 (pt0) outliers start: 23 outliers final: 19 residues processed: 122 average time/residue: 0.1663 time to fit residues: 27.2094 Evaluate side-chains 116 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105763 restraints weight = 9049.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109217 restraints weight = 5023.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111547 restraints weight = 3423.330| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6011 Z= 0.232 Angle : 0.660 10.989 8264 Z= 0.326 Chirality : 0.040 0.180 946 Planarity : 0.004 0.046 936 Dihedral : 15.531 88.793 1178 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.00 % Allowed : 28.35 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.35), residues: 628 helix: 1.54 (0.32), residues: 294 sheet: -1.78 (0.56), residues: 83 loop : -1.83 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 646 HIS 0.006 0.001 HIS A 280 PHE 0.029 0.002 PHE A 471 TYR 0.035 0.001 TYR A 548 ARG 0.011 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.31 seconds wall clock time: 27 minutes 43.74 seconds (1663.74 seconds total)