Starting phenix.real_space_refine on Sun Mar 10 19:24:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyz_15029/03_2024/7zyz_15029_updated.pdb" } resolution = 2.47 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= 0.010 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 19 5.16 5 C 2740 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4349 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4349 Unusual residues: {' MN': 1, 'OAA': 1} Classifications: {'peptide': 541, 'undetermined': 2, 'water': 38} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 515, None: 40} Not linked: pdbres="GLY A1000 " pdbres=" MN A1201 " Not linked: pdbres=" MN A1201 " pdbres="OAA A1202 " Not linked: pdbres="OAA A1202 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " Not linked: pdbres="HOH A1302 " pdbres="HOH A1303 " ... (remaining 35 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.71 Number of scatterers: 4349 At special positions: 0 Unit cell: (73.14, 77.38, 80.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 19 16.00 O 858 8.00 N 731 7.00 C 2740 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: 2.03 Conformation dependent library (CDL) restraints added in 837.9 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 50.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 503 through 521 removed outlier: 8.050A pdb=" N ALA A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ASP A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.801A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.502A pdb=" N THR A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.567A pdb=" N TYR A 775 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.518A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 818 through 821 Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 844 through 859 removed outlier: 4.194A pdb=" N ASP A 847 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 849 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 850 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 856 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 857 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 920 through 926 Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.908A pdb=" N LYS A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 985 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 994 through 999 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= B, first strand: chain 'A' and resid 728 through 731 removed outlier: 6.338A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 2.10 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: 1426 1.34 - 1.46: 731 1.46 - 1.57: 2210 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 4404 Sorted by residual: bond pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 1.329 1.427 -0.098 1.40e-02 5.10e+03 4.94e+01 bond pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sigma weight residual 1.214 1.307 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 OAA A1202 " pdb=" O2 OAA A1202 " ideal model delta sigma weight residual 1.242 1.311 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 OAA A1202 " pdb=" O4 OAA A1202 " ideal model delta sigma weight residual 1.241 1.308 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 4399 not shown) Histogram of bond angle deviations from ideal: 84.70 - 94.57: 1 94.57 - 104.43: 78 104.43 - 114.30: 2596 114.30 - 124.16: 3206 124.16 - 134.02: 80 Bond angle restraints: 5961 Sorted by residual: angle pdb=" O VAL A 702 " pdb=" C VAL A 702 " pdb=" N KCX A 703 " ideal model delta sigma weight residual 123.00 84.70 38.30 1.60e+00 3.91e-01 5.73e+02 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA LYS A 501 " pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.28e+00 angle pdb=" N ALA A 837 " pdb=" CA ALA A 837 " pdb=" C ALA A 837 " ideal model delta sigma weight residual 112.72 109.10 3.62 1.28e+00 6.10e-01 7.99e+00 ... (remaining 5956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2517 32.62 - 65.24: 118 65.24 - 97.86: 13 97.86 - 130.48: 0 130.48 - 163.10: 1 Dihedral angle restraints: 2649 sinusoidal: 1080 harmonic: 1569 Sorted by residual: dihedral pdb=" C1 OAA A1202 " pdb=" C2 OAA A1202 " pdb=" C3 OAA A1202 " pdb=" O3 OAA A1202 " ideal model delta sinusoidal sigma weight residual -102.23 60.87 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA ASN A 609 " pdb=" C ASN A 609 " pdb=" N ALA A 610 " pdb=" CA ALA A 610 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET A 648 " pdb=" C MET A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 322 0.031 - 0.062: 203 0.062 - 0.093: 90 0.093 - 0.124: 28 0.124 - 0.155: 7 Chirality restraints: 650 Sorted by residual: chirality pdb=" CG LEU A 645 " pdb=" CB LEU A 645 " pdb=" CD1 LEU A 645 " pdb=" CD2 LEU A 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA LYS A 500 " pdb=" N LYS A 500 " pdb=" C LYS A 500 " pdb=" CB LYS A 500 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA THR A 994 " pdb=" N THR A 994 " pdb=" C THR A 994 " pdb=" CB THR A 994 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 647 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 702 " 0.143 2.00e-02 2.50e+03 2.27e-01 5.14e+02 pdb=" C VAL A 702 " -0.390 2.00e-02 2.50e+03 pdb=" O VAL A 702 " 0.156 2.00e-02 2.50e+03 pdb=" N KCX A 703 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 501 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LYS A 501 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 501 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 502 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 867 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO A 868 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 868 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 868 " -0.019 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 61 2.56 - 3.14: 3641 3.14 - 3.73: 7568 3.73 - 4.31: 10735 4.31 - 4.90: 16729 Nonbonded interactions: 38734 Sorted by model distance: nonbonded pdb=" OQ2 KCX A 703 " pdb="MN MN A1201 " model vdw 1.973 2.320 nonbonded pdb="MN MN A1201 " pdb=" O HOH A1320 " model vdw 2.002 2.320 nonbonded pdb=" NE2 HIS A 734 " pdb="MN MN A1201 " model vdw 2.030 2.400 nonbonded pdb=" OD2 ASP A 534 " pdb="MN MN A1201 " model vdw 2.143 2.320 nonbonded pdb=" O HIS A 823 " pdb=" ND1 HIS A 823 " model vdw 2.151 2.520 ... (remaining 38729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 5.430 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.007 0.098 4404 Z= 0.479 Angle : 0.871 38.295 5961 Z= 0.491 Chirality : 0.047 0.155 650 Planarity : 0.009 0.227 780 Dihedral : 18.664 163.102 1645 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.45 % Allowed : 18.95 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.36), residues: 536 helix: -0.09 (0.30), residues: 294 sheet: -0.53 (0.73), residues: 43 loop : 0.14 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 799 HIS 0.003 0.001 HIS A 844 PHE 0.018 0.002 PHE A 879 TYR 0.013 0.002 TYR A 715 ARG 0.003 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 0.534 Fit side-chains REVERT: A 460 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5987 (mmt-90) outliers start: 25 outliers final: 24 residues processed: 60 average time/residue: 1.0590 time to fit residues: 66.7440 Evaluate side-chains 58 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 33 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4404 Z= 0.244 Angle : 0.514 5.875 5961 Z= 0.274 Chirality : 0.042 0.129 650 Planarity : 0.003 0.039 780 Dihedral : 10.504 159.728 644 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.14 % Allowed : 19.39 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.36), residues: 536 helix: 0.45 (0.31), residues: 282 sheet: -0.60 (0.69), residues: 43 loop : 0.50 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.001 HIS A 823 PHE 0.017 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 33 time to evaluate : 0.537 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 48 average time/residue: 1.0456 time to fit residues: 52.9266 Evaluate side-chains 39 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4404 Z= 0.250 Angle : 0.503 5.174 5961 Z= 0.267 Chirality : 0.042 0.130 650 Planarity : 0.003 0.037 780 Dihedral : 9.262 156.824 606 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.61 % Allowed : 20.70 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.54 (0.37), residues: 536 helix: 0.61 (0.31), residues: 285 sheet: -0.67 (0.69), residues: 43 loop : 0.48 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.001 HIS A 698 PHE 0.016 0.002 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.492 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 43 average time/residue: 0.9840 time to fit residues: 44.6428 Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 46 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4404 Z= 0.304 Angle : 0.529 5.235 5961 Z= 0.282 Chirality : 0.043 0.133 650 Planarity : 0.003 0.037 780 Dihedral : 9.313 157.207 604 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.27 % Allowed : 20.48 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.55 (0.37), residues: 536 helix: 0.63 (0.32), residues: 286 sheet: -0.65 (0.69), residues: 43 loop : 0.48 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.001 HIS A 999 PHE 0.016 0.002 PHE A 879 TYR 0.009 0.002 TYR A 684 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 33 time to evaluate : 0.534 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 45 average time/residue: 1.0150 time to fit residues: 48.1146 Evaluate side-chains 37 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4404 Z= 0.238 Angle : 0.495 5.157 5961 Z= 0.264 Chirality : 0.041 0.129 650 Planarity : 0.003 0.036 780 Dihedral : 9.159 155.395 604 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.14 % Allowed : 19.61 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.66 (0.37), residues: 536 helix: 0.73 (0.32), residues: 285 sheet: -0.63 (0.69), residues: 43 loop : 0.52 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.001 HIS A 698 PHE 0.016 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 34 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 691 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6679 (tp30) outliers start: 19 outliers final: 10 residues processed: 51 average time/residue: 0.9179 time to fit residues: 49.7809 Evaluate side-chains 43 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 963 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 50.0000 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4404 Z= 0.298 Angle : 0.567 9.645 5961 Z= 0.293 Chirality : 0.043 0.143 650 Planarity : 0.003 0.037 780 Dihedral : 9.260 156.476 604 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.36 % Allowed : 20.04 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.56 (0.37), residues: 536 helix: 0.66 (0.32), residues: 286 sheet: -0.67 (0.68), residues: 43 loop : 0.46 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.003 0.001 HIS A 536 PHE 0.016 0.002 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.002 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 32 time to evaluate : 0.555 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 49 average time/residue: 0.8860 time to fit residues: 45.9745 Evaluate side-chains 41 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 963 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4404 Z= 0.246 Angle : 0.531 7.610 5961 Z= 0.276 Chirality : 0.042 0.132 650 Planarity : 0.003 0.037 780 Dihedral : 9.162 155.379 604 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.70 % Allowed : 20.26 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.60 (0.37), residues: 536 helix: 0.70 (0.32), residues: 285 sheet: -0.65 (0.68), residues: 43 loop : 0.47 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.000 HIS A 698 PHE 0.015 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 0.542 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 48 average time/residue: 0.9888 time to fit residues: 50.0745 Evaluate side-chains 42 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4404 Z= 0.193 Angle : 0.512 7.345 5961 Z= 0.267 Chirality : 0.041 0.157 650 Planarity : 0.003 0.036 780 Dihedral : 8.957 153.338 604 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.61 % Allowed : 21.35 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.68 (0.37), residues: 536 helix: 0.75 (0.32), residues: 285 sheet: -0.63 (0.69), residues: 43 loop : 0.53 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.000 HIS A 698 PHE 0.015 0.001 PHE A 879 TYR 0.009 0.001 TYR A 684 ARG 0.001 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 43 average time/residue: 0.9028 time to fit residues: 41.2869 Evaluate side-chains 41 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 963 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 50.0000 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4404 Z= 0.223 Angle : 0.530 7.119 5961 Z= 0.274 Chirality : 0.041 0.129 650 Planarity : 0.003 0.035 780 Dihedral : 8.994 153.231 604 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.49 % Allowed : 21.35 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.63 (0.37), residues: 536 helix: 0.69 (0.31), residues: 285 sheet: -0.59 (0.70), residues: 43 loop : 0.51 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.000 HIS A 536 PHE 0.015 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 30 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 44 average time/residue: 0.9976 time to fit residues: 46.4628 Evaluate side-chains 42 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 963 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4404 Z= 0.186 Angle : 0.502 7.050 5961 Z= 0.262 Chirality : 0.040 0.128 650 Planarity : 0.003 0.035 780 Dihedral : 8.847 151.638 604 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 21.79 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.70 (0.37), residues: 536 helix: 0.73 (0.32), residues: 285 sheet: -0.56 (0.70), residues: 43 loop : 0.58 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.001 0.000 HIS A 698 PHE 0.014 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 845 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.543 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 43 average time/residue: 0.8858 time to fit residues: 40.5992 Evaluate side-chains 41 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 963 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.0010 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.069329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060710 restraints weight = 12099.340| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.63 r_work: 0.3058 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4404 Z= 0.209 Angle : 0.510 7.300 5961 Z= 0.267 Chirality : 0.041 0.128 650 Planarity : 0.003 0.035 780 Dihedral : 8.861 151.586 604 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 22.22 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.37), residues: 536 helix: 0.77 (0.32), residues: 285 sheet: -0.55 (0.70), residues: 43 loop : 0.56 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 569 HIS 0.002 0.000 HIS A 536 PHE 0.015 0.001 PHE A 879 TYR 0.008 0.001 TYR A 684 ARG 0.001 0.000 ARG A 845 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.12 seconds wall clock time: 31 minutes 56.09 seconds (1916.09 seconds total)