Starting phenix.real_space_refine on Tue Feb 13 12:01:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnz_26024/02_2024/7tnz_26024_updated.pdb" } resolution = 3.54 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= 0.006 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 24 5.49 5 S 33 5.16 5 C 3724 2.51 5 N 1026 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" 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: 5986 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5472 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 651} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} 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 4548 SG CYS A 810 61.041 58.191 17.936 1.00 89.32 S ATOM 4987 SG CYS A 864 59.505 57.429 14.128 1.00 94.72 S ATOM 5026 SG CYS A 869 62.267 55.718 15.502 1.00 96.38 S Time building chain proxies: 4.04, per 1000 atoms: 0.67 Number of scatterers: 5986 At special positions: 0 Unit cell: (96.12, 85.44, 82.236, 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 33 16.00 P 24 15.00 O 1178 8.00 N 1026 7.00 C 3724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 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 " 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 44.1% alpha, 6.3% beta 11 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.838A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.709A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.861A pdb=" N GLN A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) 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 396 Processing helix chain 'A' and resid 420 through 434 removed outlier: 4.078A pdb=" N ASP A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.863A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 520 Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.860A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 602 removed outlier: 3.938A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 745 through 769 removed outlier: 3.584A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) 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 837 through 840 removed outlier: 3.812A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 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 260 through 262 removed outlier: 6.983A pdb=" N VAL A 438 " --> pdb=" O ILE A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 457 through 460 removed outlier: 3.946A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 631 through 634 Processing sheet with id= D, first strand: chain 'A' and resid 659 through 661 removed outlier: 3.621A pdb=" N ILE A 695 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 842 through 845 Processing sheet with id= F, first strand: chain 'A' and resid 874 through 878 Processing sheet with id= G, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= H, first strand: chain 'A' and resid 807 through 809 212 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 1010 1.45 - 1.57: 3395 1.57 - 1.69: 45 1.69 - 1.82: 47 Bond restraints: 6154 Sorted by residual: bond pdb=" O3' 5GP B 1 " pdb=" P G B 2 " ideal model delta sigma weight residual 1.607 1.718 -0.111 1.50e-02 4.44e+03 5.48e+01 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.06e-02 8.90e+03 1.04e+01 bond pdb=" N ILE A 704 " pdb=" CA ILE A 704 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" CA ALA A 700 " pdb=" CB ALA A 700 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.56e-02 4.11e+03 9.69e+00 bond pdb=" CA SER A 437 " pdb=" CB SER A 437 " ideal model delta sigma weight residual 1.537 1.494 0.043 1.38e-02 5.25e+03 9.58e+00 ... (remaining 6149 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.67: 285 106.67 - 113.56: 3395 113.56 - 120.45: 2592 120.45 - 127.35: 2066 127.35 - 134.24: 76 Bond angle restraints: 8414 Sorted by residual: angle pdb=" C3' 5GP B 1 " pdb=" O3' 5GP B 1 " pdb=" P G B 2 " ideal model delta sigma weight residual 120.20 114.04 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" N SER A 743 " pdb=" CA SER A 743 " pdb=" C SER A 743 " ideal model delta sigma weight residual 114.04 109.57 4.47 1.24e+00 6.50e-01 1.30e+01 angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.24 122.81 -3.57 1.04e+00 9.25e-01 1.18e+01 angle pdb=" N ALA A 684 " pdb=" CA ALA A 684 " pdb=" C ALA A 684 " ideal model delta sigma weight residual 112.93 109.14 3.79 1.12e+00 7.97e-01 1.14e+01 angle pdb=" O ILE A 499 " pdb=" C ILE A 499 " pdb=" N GLN A 500 " ideal model delta sigma weight residual 121.85 124.37 -2.52 7.60e-01 1.73e+00 1.10e+01 ... (remaining 8409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3442 17.67 - 35.35: 254 35.35 - 53.02: 58 53.02 - 70.70: 41 70.70 - 88.37: 14 Dihedral angle restraints: 3809 sinusoidal: 1814 harmonic: 1995 Sorted by residual: dihedral pdb=" CA ARG A 859 " pdb=" C ARG A 859 " pdb=" N ALA A 860 " pdb=" CA ALA A 860 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB GLU A 621 " pdb=" CG GLU A 621 " pdb=" CD GLU A 621 " pdb=" OE1 GLU A 621 " ideal model delta sinusoidal sigma weight residual 0.00 87.94 -87.94 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 591 " pdb=" CG GLU A 591 " pdb=" CD GLU A 591 " pdb=" OE1 GLU A 591 " ideal model delta sinusoidal sigma weight residual 0.00 -86.22 86.22 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 3806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 400 0.041 - 0.082: 294 0.082 - 0.123: 207 0.123 - 0.164: 48 0.164 - 0.204: 5 Chirality restraints: 954 Sorted by residual: chirality pdb=" C3' 5GP B 1 " pdb=" C2' 5GP B 1 " pdb=" C4' 5GP B 1 " pdb=" O3' 5GP B 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE A 856 " pdb=" N PHE A 856 " pdb=" C PHE A 856 " pdb=" CB PHE A 856 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 951 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 11 " -0.015 2.00e-02 2.50e+03 1.30e-02 3.81e+00 pdb=" N1 C B 11 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B 11 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C B 11 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C B 11 " 0.014 2.00e-02 2.50e+03 pdb=" C4 C B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C B 11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B 11 " -0.009 2.00e-02 2.50e+03 pdb=" C6 C B 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.015 2.00e-02 2.50e+03 9.11e-03 2.49e+00 pdb=" N9 G B 9 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G B 9 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 9 " -0.009 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G B 9 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 9 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 527 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ASP A 527 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 882 2.79 - 3.32: 6177 3.32 - 3.84: 9776 3.84 - 4.37: 11617 4.37 - 4.90: 19116 Nonbonded interactions: 47568 Sorted by model distance: nonbonded pdb=" O ALA A 558 " pdb=" ND2 ASN A 608 " model vdw 2.258 2.520 nonbonded pdb=" O THR A 697 " pdb=" OG1 THR A 697 " model vdw 2.272 2.440 nonbonded pdb=" O LYS A 379 " pdb=" OP1 G B 5 " model vdw 2.286 3.040 nonbonded pdb=" N ASP A 701 " pdb=" OD1 ASP A 701 " model vdw 2.311 2.520 nonbonded pdb=" O CYS A 374 " pdb=" OG1 THR A 377 " model vdw 2.342 2.440 ... (remaining 47563 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.860 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.330 Find NCS groups from input model: 0.150 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.011 0.111 6154 Z= 0.710 Angle : 1.166 6.304 8414 Z= 0.855 Chirality : 0.068 0.204 954 Planarity : 0.004 0.032 991 Dihedral : 15.334 88.374 2513 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.80 % Favored : 92.75 % Rotamer: Outliers : 0.66 % Allowed : 3.45 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.29), residues: 676 helix: 0.17 (0.27), residues: 317 sheet: -4.32 (0.44), residues: 70 loop : -3.39 (0.28), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 771 HIS 0.009 0.002 HIS A 444 PHE 0.024 0.003 PHE A 856 TYR 0.017 0.003 TYR A 566 ARG 0.004 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp) REVERT: A 369 MET cc_start: 0.7175 (mtt) cc_final: 0.6896 (mtp) REVERT: A 459 PHE cc_start: 0.8451 (m-80) cc_final: 0.8059 (m-10) REVERT: A 481 ASP cc_start: 0.7992 (m-30) cc_final: 0.7644 (m-30) REVERT: A 523 PHE cc_start: 0.8105 (t80) cc_final: 0.7344 (t80) REVERT: A 550 ASP cc_start: 0.8932 (m-30) cc_final: 0.8731 (m-30) REVERT: A 562 ASP cc_start: 0.7457 (p0) cc_final: 0.6939 (p0) REVERT: A 603 ASP cc_start: 0.8497 (t0) cc_final: 0.8012 (t0) REVERT: A 620 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8377 (mt-10) REVERT: A 625 ASN cc_start: 0.8627 (t0) cc_final: 0.8307 (t0) REVERT: A 759 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7737 (mttt) REVERT: A 845 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7155 (mtt90) outliers start: 4 outliers final: 1 residues processed: 141 average time/residue: 0.2123 time to fit residues: 37.9305 Evaluate side-chains 97 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 299 GLN A 341 ASN A 354 ASN A 500 GLN A 678 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6154 Z= 0.189 Angle : 0.520 7.679 8414 Z= 0.257 Chirality : 0.038 0.161 954 Planarity : 0.004 0.037 991 Dihedral : 14.063 83.464 1118 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % Rotamer: Outliers : 2.30 % Allowed : 11.18 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.32), residues: 676 helix: 1.16 (0.29), residues: 325 sheet: -4.01 (0.45), residues: 85 loop : -2.83 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 873 HIS 0.008 0.001 HIS A 280 PHE 0.021 0.001 PHE A 616 TYR 0.010 0.001 TYR A 879 ARG 0.002 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.672 Fit side-chains REVERT: A 369 MET cc_start: 0.7418 (mtt) cc_final: 0.7112 (mtp) REVERT: A 387 MET cc_start: 0.8784 (mmm) cc_final: 0.8565 (mmm) REVERT: A 459 PHE cc_start: 0.8566 (m-80) cc_final: 0.8105 (m-10) REVERT: A 481 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (m-30) REVERT: A 523 PHE cc_start: 0.8192 (t80) cc_final: 0.7507 (t80) REVERT: A 525 MET cc_start: 0.7184 (mtm) cc_final: 0.6907 (mtm) REVERT: A 547 LYS cc_start: 0.8549 (tppt) cc_final: 0.8214 (mmtm) REVERT: A 602 ARG cc_start: 0.8956 (mtm110) cc_final: 0.8646 (tpp80) REVERT: A 603 ASP cc_start: 0.8556 (t0) cc_final: 0.7914 (t0) REVERT: A 625 ASN cc_start: 0.8585 (t0) cc_final: 0.8182 (t0) REVERT: A 845 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7066 (mtt90) REVERT: A 895 GLU cc_start: 0.7532 (tp30) cc_final: 0.7271 (tp30) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.1937 time to fit residues: 26.8373 Evaluate side-chains 93 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6154 Z= 0.388 Angle : 0.632 8.178 8414 Z= 0.316 Chirality : 0.042 0.164 954 Planarity : 0.004 0.042 991 Dihedral : 14.129 78.628 1118 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.73 % Favored : 91.12 % Rotamer: Outliers : 3.29 % Allowed : 14.64 % Favored : 82.07 % 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: -1.48 (0.33), residues: 676 helix: 1.14 (0.29), residues: 325 sheet: -3.65 (0.44), residues: 104 loop : -2.68 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 873 HIS 0.008 0.002 HIS A 623 PHE 0.021 0.002 PHE A 856 TYR 0.017 0.002 TYR A 717 ARG 0.003 0.001 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.691 Fit side-chains REVERT: A 435 ASP cc_start: 0.8763 (t0) cc_final: 0.8553 (t0) REVERT: A 459 PHE cc_start: 0.8790 (m-80) cc_final: 0.8306 (m-10) REVERT: A 481 ASP cc_start: 0.7980 (m-30) cc_final: 0.7661 (m-30) REVERT: A 523 PHE cc_start: 0.8176 (t80) cc_final: 0.7523 (t80) REVERT: A 550 ASP cc_start: 0.8944 (m-30) cc_final: 0.8669 (m-30) REVERT: A 602 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8732 (tpp80) REVERT: A 603 ASP cc_start: 0.8548 (t0) cc_final: 0.7932 (t0) REVERT: A 845 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7129 (mtt90) REVERT: A 895 GLU cc_start: 0.7606 (tp30) cc_final: 0.7147 (tp30) outliers start: 20 outliers final: 13 residues processed: 100 average time/residue: 0.1859 time to fit residues: 24.5054 Evaluate side-chains 87 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6154 Z= 0.263 Angle : 0.553 8.051 8414 Z= 0.274 Chirality : 0.039 0.150 954 Planarity : 0.004 0.044 991 Dihedral : 14.136 75.959 1118 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.69 % Favored : 92.16 % Rotamer: Outliers : 4.11 % Allowed : 15.95 % Favored : 79.93 % 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: -1.22 (0.34), residues: 676 helix: 1.40 (0.29), residues: 324 sheet: -3.55 (0.45), residues: 104 loop : -2.59 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 873 HIS 0.009 0.001 HIS A 623 PHE 0.027 0.002 PHE A 616 TYR 0.012 0.001 TYR A 390 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.605 Fit side-chains REVERT: A 481 ASP cc_start: 0.7963 (m-30) cc_final: 0.7623 (m-30) REVERT: A 523 PHE cc_start: 0.8126 (t80) cc_final: 0.7381 (t80) REVERT: A 550 ASP cc_start: 0.8939 (m-30) cc_final: 0.8649 (m-30) REVERT: A 602 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8727 (tpp80) REVERT: A 603 ASP cc_start: 0.8630 (t0) cc_final: 0.8002 (t0) REVERT: A 655 PHE cc_start: 0.7931 (p90) cc_final: 0.7287 (p90) REVERT: A 845 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7141 (mtt90) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 0.1725 time to fit residues: 23.2477 Evaluate side-chains 86 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6154 Z= 0.175 Angle : 0.513 8.715 8414 Z= 0.251 Chirality : 0.038 0.156 954 Planarity : 0.004 0.048 991 Dihedral : 14.092 73.845 1118 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 4.11 % Allowed : 17.11 % Favored : 78.78 % 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: -0.92 (0.34), residues: 676 helix: 1.68 (0.30), residues: 324 sheet: -3.71 (0.48), residues: 93 loop : -2.45 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 873 HIS 0.008 0.001 HIS A 623 PHE 0.030 0.001 PHE A 616 TYR 0.012 0.001 TYR A 390 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.720 Fit side-chains REVERT: A 374 CYS cc_start: 0.8508 (p) cc_final: 0.8180 (p) REVERT: A 459 PHE cc_start: 0.8810 (m-80) cc_final: 0.8364 (m-10) REVERT: A 481 ASP cc_start: 0.7982 (m-30) cc_final: 0.7626 (m-30) REVERT: A 523 PHE cc_start: 0.8173 (t80) cc_final: 0.7457 (t80) REVERT: A 550 ASP cc_start: 0.8909 (m-30) cc_final: 0.8626 (m-30) REVERT: A 602 ARG cc_start: 0.9001 (mtm110) cc_final: 0.8694 (tpp80) REVERT: A 603 ASP cc_start: 0.8609 (t0) cc_final: 0.8012 (t0) REVERT: A 655 PHE cc_start: 0.7937 (p90) cc_final: 0.7389 (p90) REVERT: A 706 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6648 (mp) REVERT: A 845 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7167 (mtt90) REVERT: A 895 GLU cc_start: 0.7695 (tp30) cc_final: 0.7405 (tp30) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 0.1777 time to fit residues: 25.1613 Evaluate side-chains 96 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6154 Z= 0.284 Angle : 0.552 8.545 8414 Z= 0.276 Chirality : 0.040 0.158 954 Planarity : 0.004 0.049 991 Dihedral : 14.133 73.746 1118 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.45 % Allowed : 18.59 % Favored : 77.96 % 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: -0.94 (0.34), residues: 676 helix: 1.59 (0.30), residues: 324 sheet: -3.62 (0.47), residues: 94 loop : -2.37 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 873 HIS 0.008 0.002 HIS A 280 PHE 0.034 0.002 PHE A 616 TYR 0.011 0.001 TYR A 390 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.693 Fit side-chains REVERT: A 374 CYS cc_start: 0.8501 (p) cc_final: 0.8125 (p) REVERT: A 481 ASP cc_start: 0.7984 (m-30) cc_final: 0.7625 (m-30) REVERT: A 523 PHE cc_start: 0.8248 (t80) cc_final: 0.7603 (t80) REVERT: A 550 ASP cc_start: 0.8959 (m-30) cc_final: 0.8665 (m-30) REVERT: A 602 ARG cc_start: 0.8976 (mtm110) cc_final: 0.8628 (tpp80) REVERT: A 603 ASP cc_start: 0.8614 (t0) cc_final: 0.8095 (t0) REVERT: A 655 PHE cc_start: 0.7935 (p90) cc_final: 0.7392 (p90) REVERT: A 845 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7134 (mtt90) outliers start: 21 outliers final: 19 residues processed: 93 average time/residue: 0.1629 time to fit residues: 20.7335 Evaluate side-chains 97 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6154 Z= 0.165 Angle : 0.495 7.782 8414 Z= 0.244 Chirality : 0.038 0.162 954 Planarity : 0.004 0.054 991 Dihedral : 14.103 73.863 1118 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.11 % Allowed : 18.91 % Favored : 76.97 % 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: -0.73 (0.35), residues: 676 helix: 1.81 (0.30), residues: 324 sheet: -3.59 (0.46), residues: 98 loop : -2.27 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 873 HIS 0.008 0.001 HIS A 280 PHE 0.031 0.001 PHE A 616 TYR 0.012 0.001 TYR A 390 ARG 0.003 0.000 ARG A 664 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.795 Fit side-chains REVERT: A 374 CYS cc_start: 0.8565 (p) cc_final: 0.8209 (p) REVERT: A 459 PHE cc_start: 0.8797 (m-80) cc_final: 0.8456 (m-80) REVERT: A 481 ASP cc_start: 0.7963 (m-30) cc_final: 0.7617 (m-30) REVERT: A 523 PHE cc_start: 0.8227 (t80) cc_final: 0.7627 (t80) REVERT: A 550 ASP cc_start: 0.8925 (m-30) cc_final: 0.8618 (m-30) REVERT: A 602 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8691 (tpp80) REVERT: A 603 ASP cc_start: 0.8627 (t0) cc_final: 0.8016 (t0) REVERT: A 655 PHE cc_start: 0.7960 (p90) cc_final: 0.7464 (p90) REVERT: A 895 GLU cc_start: 0.7735 (tp30) cc_final: 0.7294 (tp30) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.1658 time to fit residues: 22.9829 Evaluate side-chains 99 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6154 Z= 0.157 Angle : 0.499 7.398 8414 Z= 0.246 Chirality : 0.038 0.154 954 Planarity : 0.003 0.053 991 Dihedral : 14.071 73.837 1116 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.29 % Allowed : 19.74 % Favored : 76.97 % 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: -0.61 (0.35), residues: 676 helix: 1.87 (0.30), residues: 324 sheet: -3.46 (0.47), residues: 98 loop : -2.18 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 873 HIS 0.006 0.001 HIS A 280 PHE 0.036 0.001 PHE A 616 TYR 0.013 0.001 TYR A 473 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.698 Fit side-chains REVERT: A 374 CYS cc_start: 0.8504 (p) cc_final: 0.8146 (p) REVERT: A 459 PHE cc_start: 0.8820 (m-80) cc_final: 0.8517 (m-80) REVERT: A 481 ASP cc_start: 0.7978 (m-30) cc_final: 0.7630 (m-30) REVERT: A 523 PHE cc_start: 0.8150 (t80) cc_final: 0.7574 (t80) REVERT: A 550 ASP cc_start: 0.8928 (m-30) cc_final: 0.8619 (m-30) REVERT: A 602 ARG cc_start: 0.9002 (mtm110) cc_final: 0.8702 (tpp80) REVERT: A 603 ASP cc_start: 0.8584 (t0) cc_final: 0.8016 (t0) REVERT: A 655 PHE cc_start: 0.8008 (p90) cc_final: 0.7517 (p90) REVERT: A 706 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 895 GLU cc_start: 0.7709 (tp30) cc_final: 0.7176 (tp30) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.1561 time to fit residues: 21.4886 Evaluate side-chains 96 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6154 Z= 0.228 Angle : 0.532 7.688 8414 Z= 0.262 Chirality : 0.039 0.145 954 Planarity : 0.004 0.055 991 Dihedral : 14.090 73.781 1116 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.62 % Allowed : 19.08 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.35), residues: 676 helix: 1.80 (0.30), residues: 323 sheet: -3.40 (0.47), residues: 97 loop : -2.18 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 873 HIS 0.006 0.001 HIS A 623 PHE 0.012 0.001 PHE A 856 TYR 0.012 0.001 TYR A 390 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.570 Fit side-chains REVERT: A 374 CYS cc_start: 0.8478 (p) cc_final: 0.8100 (p) REVERT: A 459 PHE cc_start: 0.8787 (m-80) cc_final: 0.8458 (m-80) REVERT: A 481 ASP cc_start: 0.8008 (m-30) cc_final: 0.7646 (m-30) REVERT: A 523 PHE cc_start: 0.8186 (t80) cc_final: 0.7626 (t80) REVERT: A 550 ASP cc_start: 0.8962 (m-30) cc_final: 0.8633 (m-30) REVERT: A 602 ARG cc_start: 0.8971 (mtm110) cc_final: 0.8716 (tpp80) REVERT: A 603 ASP cc_start: 0.8629 (t0) cc_final: 0.8016 (t0) REVERT: A 646 TRP cc_start: 0.8671 (t60) cc_final: 0.8439 (t60) REVERT: A 655 PHE cc_start: 0.7976 (p90) cc_final: 0.7454 (p90) REVERT: A 706 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6759 (mp) outliers start: 22 outliers final: 20 residues processed: 96 average time/residue: 0.1561 time to fit residues: 21.0414 Evaluate side-chains 98 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6154 Z= 0.165 Angle : 0.515 7.761 8414 Z= 0.252 Chirality : 0.039 0.170 954 Planarity : 0.004 0.057 991 Dihedral : 14.087 73.878 1116 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.45 % Allowed : 19.57 % Favored : 76.97 % 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: -0.53 (0.35), residues: 676 helix: 1.92 (0.30), residues: 323 sheet: -3.35 (0.47), residues: 97 loop : -2.15 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 873 HIS 0.008 0.001 HIS A 623 PHE 0.042 0.001 PHE A 616 TYR 0.029 0.001 TYR A 473 ARG 0.002 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.672 Fit side-chains REVERT: A 374 CYS cc_start: 0.8551 (p) cc_final: 0.8208 (p) REVERT: A 459 PHE cc_start: 0.8773 (m-80) cc_final: 0.8498 (m-80) REVERT: A 481 ASP cc_start: 0.8035 (m-30) cc_final: 0.7686 (m-30) REVERT: A 523 PHE cc_start: 0.8185 (t80) cc_final: 0.7592 (t80) REVERT: A 550 ASP cc_start: 0.8931 (m-30) cc_final: 0.8616 (m-30) REVERT: A 602 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8708 (tpp80) REVERT: A 603 ASP cc_start: 0.8583 (t0) cc_final: 0.7999 (t0) REVERT: A 646 TRP cc_start: 0.8661 (t60) cc_final: 0.8436 (t60) REVERT: A 655 PHE cc_start: 0.8006 (p90) cc_final: 0.7507 (p90) REVERT: A 706 ILE cc_start: 0.7002 (pt) cc_final: 0.6787 (mp) outliers start: 21 outliers final: 20 residues processed: 98 average time/residue: 0.1579 time to fit residues: 21.4093 Evaluate side-chains 100 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116179 restraints weight = 7698.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120042 restraints weight = 5107.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122367 restraints weight = 4081.916| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 6154 Z= 0.214 Angle : 0.997 59.199 8414 Z= 0.576 Chirality : 0.040 0.369 954 Planarity : 0.004 0.056 991 Dihedral : 14.099 73.874 1116 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.62 % Allowed : 19.08 % Favored : 77.30 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.35), residues: 676 helix: 1.92 (0.30), residues: 323 sheet: -3.34 (0.47), residues: 97 loop : -2.13 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 646 HIS 0.011 0.001 HIS A 623 PHE 0.025 0.002 PHE A 616 TYR 0.024 0.001 TYR A 473 ARG 0.005 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.15 seconds wall clock time: 27 minutes 4.33 seconds (1624.33 seconds total)