Starting phenix.real_space_refine on Sun Mar 10 19:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sym_40884/03_2024/8sym_40884.pdb" } resolution = 3.2 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2878 2.51 5 N 772 2.21 5 O 809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4486 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3023 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175} Time building chain proxies: 3.01, per 1000 atoms: 0.67 Number of scatterers: 4486 At special positions: 0 Unit cell: (76.4928, 89.2416, 74.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 809 8.00 N 772 7.00 C 2878 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: 1.76 Conformation dependent library (CDL) restraints added in 916.7 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1066 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 54.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 582 through 597 removed outlier: 4.084A pdb=" N CYS A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.819A pdb=" N MET A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 Processing helix chain 'A' and resid 667 through 689 removed outlier: 3.552A pdb=" N LEU A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.998A pdb=" N ALA A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 717 through 734 Processing helix chain 'A' and resid 737 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 768 through 783 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.642A pdb=" N HIS A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 853 through 882 Processing helix chain 'A' and resid 883 through 902 removed outlier: 3.653A pdb=" N GLN A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 923 removed outlier: 3.820A pdb=" N HIS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 30 removed outlier: 3.576A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.729A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.940A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.463A pdb=" N LEU B 6 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 39 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 8 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81 264 hydrogen bonds defined for protein. 768 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: 1.20 Time building geometry restraints manager: 1.92 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: 1460 1.34 - 1.46: 861 1.46 - 1.57: 2224 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4585 Sorted by residual: bond pdb=" C GLN B 93 " pdb=" N VAL B 94 " ideal model delta sigma weight residual 1.333 1.321 0.012 1.20e-02 6.94e+03 1.03e+00 bond pdb=" CB VAL B 112 " pdb=" CG2 VAL B 112 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.46e-01 bond pdb=" CG1 ILE A 805 " pdb=" CD1 ILE A 805 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.90e-01 bond pdb=" N VAL B 63 " pdb=" CA VAL B 63 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.28e-02 6.10e+03 5.91e-01 bond pdb=" CA HIS A 901 " pdb=" CB HIS A 901 " ideal model delta sigma weight residual 1.537 1.524 0.012 1.67e-02 3.59e+03 5.37e-01 ... (remaining 4580 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.84: 126 106.84 - 113.61: 2590 113.61 - 120.38: 1677 120.38 - 127.15: 1756 127.15 - 133.92: 52 Bond angle restraints: 6201 Sorted by residual: angle pdb=" C LEU B 44 " pdb=" N CYS B 45 " pdb=" CA CYS B 45 " ideal model delta sigma weight residual 121.54 128.64 -7.10 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C VAL A 752 " pdb=" CA VAL A 752 " pdb=" CB VAL A 752 " ideal model delta sigma weight residual 113.70 110.33 3.37 9.50e-01 1.11e+00 1.26e+01 angle pdb=" N GLY B 118 " pdb=" CA GLY B 118 " pdb=" C GLY B 118 " ideal model delta sigma weight residual 113.18 120.08 -6.90 2.37e+00 1.78e-01 8.47e+00 angle pdb=" C ALA A 900 " pdb=" N HIS A 901 " pdb=" CA HIS A 901 " ideal model delta sigma weight residual 122.42 118.86 3.56 1.77e+00 3.19e-01 4.03e+00 angle pdb=" C LEU A 751 " pdb=" N VAL A 752 " pdb=" CA VAL A 752 " ideal model delta sigma weight residual 120.43 122.23 -1.80 9.60e-01 1.09e+00 3.51e+00 ... (remaining 6196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2466 16.30 - 32.61: 218 32.61 - 48.91: 57 48.91 - 65.21: 4 65.21 - 81.52: 6 Dihedral angle restraints: 2751 sinusoidal: 1110 harmonic: 1641 Sorted by residual: dihedral pdb=" CA MET A 689 " pdb=" C MET A 689 " pdb=" N LYS A 690 " pdb=" CA LYS A 690 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA HIS A 33 " pdb=" C HIS A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TYR A 32 " pdb=" C TYR A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 443 0.034 - 0.068: 168 0.068 - 0.101: 57 0.101 - 0.135: 30 0.135 - 0.169: 2 Chirality restraints: 700 Sorted by residual: chirality pdb=" CB ILE A 718 " pdb=" CA ILE A 718 " pdb=" CG1 ILE A 718 " pdb=" CG2 ILE A 718 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 761 " pdb=" N ILE A 761 " pdb=" C ILE A 761 " pdb=" CB ILE A 761 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 697 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 15 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 16 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 712 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 713 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 33 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 34 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " -0.017 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 948 2.78 - 3.31: 4419 3.31 - 3.84: 7481 3.84 - 4.37: 8784 4.37 - 4.90: 14699 Nonbonded interactions: 36331 Sorted by model distance: nonbonded pdb=" NE2 GLN A 806 " pdb=" OH TYR A 821 " model vdw 2.253 2.520 nonbonded pdb=" NH1 ARG A 11 " pdb=" OD1 ASP B 99 " model vdw 2.301 2.520 nonbonded pdb=" O PRO A 756 " pdb=" OG SER A 768 " model vdw 2.322 2.440 nonbonded pdb=" NH2 ARG A 11 " pdb=" OE1 GLU A 16 " model vdw 2.356 2.520 nonbonded pdb=" NE2 HIS A 839 " pdb=" OD2 ASP A 847 " model vdw 2.357 2.520 ... (remaining 36326 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: 1.200 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: 5.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4585 Z= 0.287 Angle : 0.542 7.096 6201 Z= 0.301 Chirality : 0.044 0.169 700 Planarity : 0.004 0.042 790 Dihedral : 13.673 81.517 1685 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.78 (0.35), residues: 552 helix: 1.99 (0.31), residues: 289 sheet: 1.00 (0.69), residues: 61 loop : 0.13 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 6 HIS 0.007 0.001 HIS A 33 PHE 0.013 0.002 PHE A 744 TYR 0.011 0.002 TYR A 725 ARG 0.002 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7074 (mt-10) REVERT: A 598 GLN cc_start: 0.8058 (mp-120) cc_final: 0.7788 (mm-40) REVERT: A 602 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8065 (mtpp) REVERT: A 642 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7654 (ttmm) REVERT: A 661 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7639 (tmm-80) REVERT: A 679 ASN cc_start: 0.7791 (m-40) cc_final: 0.7147 (m-40) REVERT: A 696 LYS cc_start: 0.8158 (mttt) cc_final: 0.7949 (mttt) REVERT: A 825 LEU cc_start: 0.8791 (mt) cc_final: 0.8560 (mp) REVERT: A 855 LYS cc_start: 0.7823 (mtpt) cc_final: 0.7184 (mtpt) REVERT: A 862 LYS cc_start: 0.8188 (tppt) cc_final: 0.7735 (tppt) REVERT: A 881 ASP cc_start: 0.7609 (m-30) cc_final: 0.7285 (m-30) REVERT: A 894 PHE cc_start: 0.8616 (t80) cc_final: 0.8137 (t80) REVERT: A 911 GLN cc_start: 0.7991 (tp40) cc_final: 0.7463 (tp40) REVERT: A 915 ASN cc_start: 0.8247 (m-40) cc_final: 0.7572 (m110) REVERT: B 105 LEU cc_start: 0.8363 (mp) cc_final: 0.8097 (mm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2269 time to fit residues: 39.8972 Evaluate side-chains 139 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 666 ASN A 673 GLN A 806 GLN A 813 ASN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 911 GLN B 4 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4585 Z= 0.243 Angle : 0.527 7.091 6201 Z= 0.279 Chirality : 0.043 0.193 700 Planarity : 0.004 0.042 790 Dihedral : 4.484 17.581 598 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.20 % Allowed : 9.62 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.81 (0.35), residues: 552 helix: 1.97 (0.30), residues: 296 sheet: 0.87 (0.69), residues: 61 loop : 0.22 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 6 HIS 0.006 0.001 HIS A 33 PHE 0.015 0.002 PHE A 779 TYR 0.009 0.001 TYR A 707 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 598 GLN cc_start: 0.8012 (mp-120) cc_final: 0.7811 (mm-40) REVERT: A 602 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8085 (mtpp) REVERT: A 642 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7646 (ttmm) REVERT: A 679 ASN cc_start: 0.7780 (m-40) cc_final: 0.7063 (m110) REVERT: A 684 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7295 (mt-10) REVERT: A 696 LYS cc_start: 0.8065 (mttt) cc_final: 0.7861 (mttt) REVERT: A 742 ASP cc_start: 0.7801 (t0) cc_final: 0.7538 (t0) REVERT: A 806 GLN cc_start: 0.7730 (tp40) cc_final: 0.7224 (tp40) REVERT: A 825 LEU cc_start: 0.8882 (mt) cc_final: 0.8541 (mp) REVERT: A 855 LYS cc_start: 0.7492 (mtpt) cc_final: 0.7045 (mtpt) REVERT: A 862 LYS cc_start: 0.8232 (tppt) cc_final: 0.7770 (tppt) REVERT: A 881 ASP cc_start: 0.7536 (m-30) cc_final: 0.7187 (m-30) REVERT: A 894 PHE cc_start: 0.8620 (t80) cc_final: 0.8209 (t80) REVERT: B 105 LEU cc_start: 0.8382 (mp) cc_final: 0.8116 (mm) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2302 time to fit residues: 37.3406 Evaluate side-chains 136 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 673 GLN A 813 ASN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4585 Z= 0.217 Angle : 0.511 6.528 6201 Z= 0.273 Chirality : 0.042 0.186 700 Planarity : 0.004 0.042 790 Dihedral : 4.420 17.013 598 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.80 % Allowed : 14.23 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.82 (0.35), residues: 552 helix: 1.97 (0.30), residues: 297 sheet: 0.76 (0.67), residues: 61 loop : 0.25 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 6 HIS 0.004 0.001 HIS A 33 PHE 0.013 0.001 PHE A 779 TYR 0.008 0.001 TYR A 707 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 602 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8090 (mtpp) REVERT: A 642 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7679 (ttmm) REVERT: A 679 ASN cc_start: 0.7785 (m-40) cc_final: 0.7066 (m110) REVERT: A 684 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 806 GLN cc_start: 0.7679 (tp40) cc_final: 0.7051 (tp-100) REVERT: A 825 LEU cc_start: 0.8872 (mt) cc_final: 0.8523 (mp) REVERT: A 855 LYS cc_start: 0.7383 (mtpt) cc_final: 0.7092 (mtpt) REVERT: A 862 LYS cc_start: 0.8259 (tppt) cc_final: 0.7754 (tppt) REVERT: A 881 ASP cc_start: 0.7531 (m-30) cc_final: 0.7187 (m-30) REVERT: A 894 PHE cc_start: 0.8622 (t80) cc_final: 0.8233 (t80) REVERT: B 105 LEU cc_start: 0.8417 (mp) cc_final: 0.8133 (mm) REVERT: B 168 VAL cc_start: 0.8456 (t) cc_final: 0.7988 (m) outliers start: 4 outliers final: 2 residues processed: 140 average time/residue: 0.2293 time to fit residues: 38.0399 Evaluate side-chains 135 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 673 GLN A 813 ASN B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4585 Z= 0.265 Angle : 0.529 6.862 6201 Z= 0.281 Chirality : 0.043 0.169 700 Planarity : 0.004 0.041 790 Dihedral : 4.431 17.784 598 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.80 % Allowed : 15.03 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.76 (0.35), residues: 552 helix: 1.95 (0.30), residues: 297 sheet: 0.67 (0.66), residues: 61 loop : 0.21 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 6 HIS 0.007 0.001 HIS A 33 PHE 0.018 0.001 PHE A 779 TYR 0.011 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7189 (mt-10) REVERT: A 602 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8086 (mtpp) REVERT: A 642 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7675 (ttmm) REVERT: A 679 ASN cc_start: 0.7789 (m-40) cc_final: 0.7073 (m110) REVERT: A 684 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 806 GLN cc_start: 0.7669 (tp40) cc_final: 0.7031 (tp-100) REVERT: A 855 LYS cc_start: 0.7395 (mtpt) cc_final: 0.7102 (mtpt) REVERT: A 862 LYS cc_start: 0.8256 (tppt) cc_final: 0.7778 (tppt) REVERT: A 881 ASP cc_start: 0.7542 (m-30) cc_final: 0.7196 (m-30) REVERT: A 894 PHE cc_start: 0.8636 (t80) cc_final: 0.8203 (t80) REVERT: B 105 LEU cc_start: 0.8458 (mp) cc_final: 0.8169 (mm) REVERT: B 168 VAL cc_start: 0.8493 (t) cc_final: 0.8022 (m) outliers start: 9 outliers final: 6 residues processed: 138 average time/residue: 0.2331 time to fit residues: 38.1636 Evaluate side-chains 141 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 813 ASN B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4585 Z= 0.283 Angle : 0.532 6.934 6201 Z= 0.286 Chirality : 0.043 0.145 700 Planarity : 0.004 0.040 790 Dihedral : 4.479 18.587 598 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.00 % Allowed : 16.23 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.69 (0.35), residues: 552 helix: 1.88 (0.30), residues: 297 sheet: 0.61 (0.66), residues: 61 loop : 0.19 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.008 0.001 HIS A 33 PHE 0.016 0.001 PHE A 779 TYR 0.012 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 602 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8068 (mtpp) REVERT: A 642 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7667 (ttmm) REVERT: A 679 ASN cc_start: 0.7781 (m-40) cc_final: 0.7073 (m110) REVERT: A 684 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 765 MET cc_start: 0.7941 (mmm) cc_final: 0.7002 (mmm) REVERT: A 806 GLN cc_start: 0.7687 (tp40) cc_final: 0.7046 (tp-100) REVERT: A 855 LYS cc_start: 0.7420 (mtpt) cc_final: 0.7118 (mtpt) REVERT: A 862 LYS cc_start: 0.8263 (tppt) cc_final: 0.7799 (tppt) REVERT: A 894 PHE cc_start: 0.8628 (t80) cc_final: 0.8231 (t80) REVERT: B 105 LEU cc_start: 0.8465 (mp) cc_final: 0.8184 (mm) REVERT: B 168 VAL cc_start: 0.8508 (t) cc_final: 0.8031 (m) outliers start: 10 outliers final: 7 residues processed: 132 average time/residue: 0.2443 time to fit residues: 37.9926 Evaluate side-chains 135 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 813 ASN B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4585 Z= 0.258 Angle : 0.533 7.490 6201 Z= 0.285 Chirality : 0.043 0.135 700 Planarity : 0.004 0.041 790 Dihedral : 4.458 18.965 598 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.40 % Allowed : 16.63 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.71 (0.35), residues: 552 helix: 1.89 (0.30), residues: 297 sheet: 0.63 (0.66), residues: 61 loop : 0.23 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 97 HIS 0.007 0.001 HIS A 33 PHE 0.014 0.001 PHE A 779 TYR 0.013 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 642 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7743 (ttmm) REVERT: A 679 ASN cc_start: 0.7768 (m-40) cc_final: 0.7067 (m110) REVERT: A 684 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 765 MET cc_start: 0.7894 (mmm) cc_final: 0.6991 (mmm) REVERT: A 806 GLN cc_start: 0.7683 (tp40) cc_final: 0.6983 (tp-100) REVERT: A 862 LYS cc_start: 0.8247 (tppt) cc_final: 0.7790 (tppt) REVERT: A 894 PHE cc_start: 0.8604 (t80) cc_final: 0.8218 (t80) REVERT: B 105 LEU cc_start: 0.8471 (mp) cc_final: 0.8188 (mm) REVERT: B 168 VAL cc_start: 0.8515 (t) cc_final: 0.8038 (m) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.2310 time to fit residues: 37.2620 Evaluate side-chains 137 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 29 optimal weight: 0.0770 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 21 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN A 813 ASN B 4 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4585 Z= 0.183 Angle : 0.508 6.261 6201 Z= 0.271 Chirality : 0.041 0.139 700 Planarity : 0.004 0.042 790 Dihedral : 4.317 18.823 598 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 18.44 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.90 (0.36), residues: 552 helix: 2.02 (0.30), residues: 297 sheet: 0.74 (0.62), residues: 71 loop : 0.33 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 6 HIS 0.004 0.001 HIS A 33 PHE 0.010 0.001 PHE A 775 TYR 0.010 0.001 TYR A 808 ARG 0.004 0.000 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 679 ASN cc_start: 0.7774 (m-40) cc_final: 0.7045 (m110) REVERT: A 684 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 765 MET cc_start: 0.7939 (mmm) cc_final: 0.7003 (mmm) REVERT: A 862 LYS cc_start: 0.8208 (tppt) cc_final: 0.7761 (tppt) REVERT: A 894 PHE cc_start: 0.8599 (t80) cc_final: 0.8185 (t80) REVERT: B 105 LEU cc_start: 0.8427 (mp) cc_final: 0.8156 (mm) REVERT: B 168 VAL cc_start: 0.8510 (t) cc_final: 0.8026 (m) outliers start: 8 outliers final: 5 residues processed: 141 average time/residue: 0.2351 time to fit residues: 39.3193 Evaluate side-chains 137 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN B 4 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4585 Z= 0.255 Angle : 0.551 6.902 6201 Z= 0.288 Chirality : 0.043 0.139 700 Planarity : 0.004 0.041 790 Dihedral : 4.397 20.047 598 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.80 % Allowed : 18.84 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.84 (0.36), residues: 552 helix: 1.96 (0.30), residues: 297 sheet: 0.88 (0.63), residues: 69 loop : 0.25 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 6 HIS 0.007 0.001 HIS A 33 PHE 0.012 0.001 PHE A 779 TYR 0.012 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 679 ASN cc_start: 0.7772 (m-40) cc_final: 0.7084 (m110) REVERT: A 684 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 806 GLN cc_start: 0.7644 (tp40) cc_final: 0.7240 (tp40) REVERT: A 862 LYS cc_start: 0.8219 (tppt) cc_final: 0.7776 (tppt) REVERT: A 894 PHE cc_start: 0.8611 (t80) cc_final: 0.8238 (t80) REVERT: B 105 LEU cc_start: 0.8451 (mp) cc_final: 0.8173 (mm) REVERT: B 168 VAL cc_start: 0.8531 (t) cc_final: 0.8061 (m) outliers start: 9 outliers final: 8 residues processed: 135 average time/residue: 0.2493 time to fit residues: 39.5952 Evaluate side-chains 137 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.0040 chunk 29 optimal weight: 0.0980 chunk 21 optimal weight: 0.0670 chunk 38 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 overall best weight: 0.0706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 673 GLN ** A 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4585 Z= 0.139 Angle : 0.514 7.753 6201 Z= 0.268 Chirality : 0.040 0.141 700 Planarity : 0.004 0.039 790 Dihedral : 4.126 19.635 598 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.40 % Allowed : 20.04 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.14 (0.36), residues: 552 helix: 2.20 (0.31), residues: 297 sheet: 0.94 (0.63), residues: 71 loop : 0.41 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 917 HIS 0.002 0.001 HIS A 826 PHE 0.012 0.001 PHE A 656 TYR 0.009 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 679 ASN cc_start: 0.7782 (m-40) cc_final: 0.7023 (m110) REVERT: A 684 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 806 GLN cc_start: 0.7536 (tp40) cc_final: 0.7334 (tp40) REVERT: A 859 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6945 (mm-30) REVERT: A 862 LYS cc_start: 0.8181 (tppt) cc_final: 0.7715 (tppt) REVERT: A 894 PHE cc_start: 0.8570 (t80) cc_final: 0.8202 (t80) REVERT: B 105 LEU cc_start: 0.8291 (mp) cc_final: 0.8023 (mm) REVERT: B 129 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 168 VAL cc_start: 0.8498 (t) cc_final: 0.8027 (m) outliers start: 7 outliers final: 4 residues processed: 135 average time/residue: 0.2443 time to fit residues: 38.7692 Evaluate side-chains 131 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN A 673 GLN A 813 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4585 Z= 0.214 Angle : 0.540 7.425 6201 Z= 0.282 Chirality : 0.042 0.143 700 Planarity : 0.004 0.037 790 Dihedral : 4.211 21.130 598 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.80 % Allowed : 21.04 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.12 (0.36), residues: 552 helix: 2.17 (0.31), residues: 297 sheet: 1.21 (0.64), residues: 69 loop : 0.31 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 6 HIS 0.006 0.001 HIS A 33 PHE 0.013 0.001 PHE B 154 TYR 0.013 0.001 TYR A 808 ARG 0.004 0.000 ARG A 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7189 (mt-10) REVERT: A 679 ASN cc_start: 0.7770 (m-40) cc_final: 0.7568 (m110) REVERT: A 684 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 765 MET cc_start: 0.7887 (mmm) cc_final: 0.7063 (mmm) REVERT: A 806 GLN cc_start: 0.7616 (tp40) cc_final: 0.7252 (tp40) REVERT: A 862 LYS cc_start: 0.8192 (tppt) cc_final: 0.7797 (tppt) REVERT: A 894 PHE cc_start: 0.8607 (t80) cc_final: 0.8230 (t80) REVERT: B 105 LEU cc_start: 0.8405 (mp) cc_final: 0.8145 (mm) REVERT: B 129 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 168 VAL cc_start: 0.8593 (t) cc_final: 0.8120 (m) outliers start: 4 outliers final: 4 residues processed: 136 average time/residue: 0.2476 time to fit residues: 39.7787 Evaluate side-chains 136 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 666 ASN A 813 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110557 restraints weight = 6640.948| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.19 r_work: 0.3319 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4585 Z= 0.308 Angle : 0.581 7.248 6201 Z= 0.307 Chirality : 0.044 0.150 700 Planarity : 0.004 0.037 790 Dihedral : 4.475 22.006 598 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.80 % Allowed : 21.44 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.86 (0.36), residues: 552 helix: 1.98 (0.30), residues: 297 sheet: 1.12 (0.64), residues: 69 loop : 0.15 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 6 HIS 0.008 0.001 HIS A 33 PHE 0.016 0.002 PHE A 779 TYR 0.015 0.001 TYR A 808 ARG 0.005 0.000 ARG A 695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.36 seconds wall clock time: 29 minutes 38.90 seconds (1778.90 seconds total)