Starting phenix.real_space_refine on Tue Nov 14 03:52:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w62_21551/11_2023/6w62_21551.pdb" } resolution = 3.9 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= 0.003 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 P 24 5.49 5 S 30 5.16 5 C 4602 2.51 5 N 1293 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7387 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6877 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 29, 'TRANS': 880} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 536 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 321 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 510 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Time building chain proxies: 4.75, per 1000 atoms: 0.64 Number of scatterers: 7387 At special positions: 0 Unit cell: (79.8, 122.85, 107.1, 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) S 30 16.00 P 24 15.00 O 1438 8.00 N 1293 7.00 C 4602 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 52.7% alpha, 6.7% beta 5 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.503A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 removed outlier: 4.085A pdb=" N TYR A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 4.363A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.913A pdb=" N GLU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 423 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.864A pdb=" N ASP A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.651A pdb=" N ARG A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 removed outlier: 4.168A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 778 removed outlier: 4.523A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.765A pdb=" N LEU A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 916 through 929 removed outlier: 3.515A pdb=" N VAL A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.534A pdb=" N GLU A 970 " --> pdb=" O THR A 967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 971 " --> pdb=" O PRO A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 971' Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.699A pdb=" N ARG A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 3.630A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 removed outlier: 3.686A pdb=" N PHE A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.517A pdb=" N ALA A 629 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.819A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.786A pdb=" N GLY A 479 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 486 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 515 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.179A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 642 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.633A pdb=" N TYR A 695 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 963 through 966 removed outlier: 3.949A pdb=" N PHE A1040 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.962A pdb=" N THR A1059 " --> pdb=" O VAL A1070 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 3.61 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: 2260 1.34 - 1.45: 1159 1.45 - 1.57: 4056 1.57 - 1.69: 47 1.69 - 1.81: 51 Bond restraints: 7573 Sorted by residual: bond pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.41e-02 5.03e+03 8.79e+00 bond pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL A 686 " pdb=" CA VAL A 686 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.91e+00 bond pdb=" N SER A 803 " pdb=" CA SER A 803 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.51e+00 ... (remaining 7568 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 298 106.89 - 113.67: 4252 113.67 - 120.46: 2925 120.46 - 127.24: 2771 127.24 - 134.03: 100 Bond angle restraints: 10346 Sorted by residual: angle pdb=" N PRO A 491 " pdb=" CA PRO A 491 " pdb=" C PRO A 491 " ideal model delta sigma weight residual 113.53 124.09 -10.56 1.39e+00 5.18e-01 5.77e+01 angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.25 110.62 -7.37 1.05e+00 9.07e-01 4.93e+01 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" CB PRO A 955 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.29e+01 angle pdb=" N PRO A 339 " pdb=" CA PRO A 339 " pdb=" CB PRO A 339 " ideal model delta sigma weight residual 103.23 110.01 -6.78 1.07e+00 8.73e-01 4.02e+01 angle pdb=" C ILE A 488 " pdb=" N ILE A 489 " pdb=" CA ILE A 489 " ideal model delta sigma weight residual 120.46 126.77 -6.31 1.37e+00 5.33e-01 2.12e+01 ... (remaining 10341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 4447 35.75 - 71.50: 84 71.50 - 107.25: 7 107.25 - 142.99: 0 142.99 - 178.74: 2 Dihedral angle restraints: 4540 sinusoidal: 1866 harmonic: 2674 Sorted by residual: dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual 232.00 53.26 178.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B -11 " pdb=" C1' C B -11 " pdb=" N1 C B -11 " pdb=" C2 C B -11 " ideal model delta sinusoidal sigma weight residual 232.00 55.42 176.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1076 0.069 - 0.137: 96 0.137 - 0.206: 6 0.206 - 0.275: 3 0.275 - 0.343: 2 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA SER A 490 " pdb=" N SER A 490 " pdb=" C SER A 490 " pdb=" CB SER A 490 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA LEU A 799 " pdb=" N LEU A 799 " pdb=" C LEU A 799 " pdb=" CB LEU A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1180 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 798 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER A 798 " -0.060 2.00e-02 2.50e+03 pdb=" O SER A 798 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 799 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 674 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 675 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 845 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ALA A 845 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 845 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 846 " 0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 78 2.49 - 3.09: 5914 3.09 - 3.69: 11592 3.69 - 4.30: 16348 4.30 - 4.90: 25760 Nonbonded interactions: 59692 Sorted by model distance: nonbonded pdb=" O2' U B -5 " pdb=" OP1 G B -4 " model vdw 1.883 2.440 nonbonded pdb=" O2' G B 1 " pdb=" O5' C B 2 " model vdw 2.064 2.440 nonbonded pdb=" N VAL A 686 " pdb=" OD1 ASP A 696 " model vdw 2.198 2.520 nonbonded pdb=" O SER A 798 " pdb=" N SER A 800 " model vdw 2.201 2.520 nonbonded pdb=" OH TYR A 473 " pdb=" O LYS A 619 " model vdw 2.204 2.440 ... (remaining 59687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.870 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7573 Z= 0.220 Angle : 0.642 10.557 10346 Z= 0.410 Chirality : 0.043 0.343 1183 Planarity : 0.004 0.074 1236 Dihedral : 14.225 178.742 2806 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.22 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.27), residues: 900 helix: 0.41 (0.25), residues: 439 sheet: -2.39 (0.50), residues: 101 loop : -3.38 (0.28), residues: 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1993 time to fit residues: 37.4353 Evaluate side-chains 109 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 459 HIS A 477 ASN A 592 GLN A 600 GLN A 771 HIS A 993 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7573 Z= 0.283 Angle : 0.717 8.981 10346 Z= 0.371 Chirality : 0.045 0.235 1183 Planarity : 0.004 0.058 1236 Dihedral : 13.224 178.772 1256 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.33 % Favored : 88.44 % Rotamer: Outliers : 2.38 % Allowed : 10.70 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.27), residues: 900 helix: 0.23 (0.24), residues: 450 sheet: -2.31 (0.56), residues: 80 loop : -3.21 (0.29), residues: 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 131 average time/residue: 0.1900 time to fit residues: 34.1159 Evaluate side-chains 117 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0708 time to fit residues: 2.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN A 407 GLN ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 7573 Z= 0.470 Angle : 0.883 9.696 10346 Z= 0.463 Chirality : 0.052 0.257 1183 Planarity : 0.006 0.064 1236 Dihedral : 13.691 175.820 1256 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.11 % Favored : 85.78 % Rotamer: Outliers : 3.71 % Allowed : 16.20 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.26), residues: 900 helix: -0.57 (0.23), residues: 455 sheet: -2.73 (0.54), residues: 77 loop : -3.46 (0.28), residues: 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 144 average time/residue: 0.1826 time to fit residues: 36.3790 Evaluate side-chains 124 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0822 time to fit residues: 2.8993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7573 Z= 0.240 Angle : 0.720 9.377 10346 Z= 0.365 Chirality : 0.046 0.243 1183 Planarity : 0.004 0.065 1236 Dihedral : 13.384 179.528 1256 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.27 % Allowed : 17.98 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.27), residues: 900 helix: -0.16 (0.23), residues: 457 sheet: -2.60 (0.54), residues: 82 loop : -3.23 (0.31), residues: 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 133 average time/residue: 0.1766 time to fit residues: 32.8578 Evaluate side-chains 127 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0690 time to fit residues: 3.1950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7573 Z= 0.194 Angle : 0.684 11.116 10346 Z= 0.344 Chirality : 0.043 0.189 1183 Planarity : 0.004 0.063 1236 Dihedral : 13.281 179.011 1256 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.67 % Allowed : 19.17 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.28), residues: 900 helix: 0.16 (0.24), residues: 458 sheet: -2.34 (0.57), residues: 80 loop : -3.13 (0.31), residues: 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 135 average time/residue: 0.1719 time to fit residues: 32.9322 Evaluate side-chains 113 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0753 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7573 Z= 0.176 Angle : 0.714 13.224 10346 Z= 0.348 Chirality : 0.045 0.357 1183 Planarity : 0.004 0.065 1236 Dihedral : 13.187 178.019 1256 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 1.93 % Allowed : 22.14 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.28), residues: 900 helix: 0.38 (0.24), residues: 456 sheet: -2.19 (0.55), residues: 91 loop : -3.10 (0.31), residues: 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.1882 time to fit residues: 32.8262 Evaluate side-chains 113 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0716 time to fit residues: 1.9206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7573 Z= 0.175 Angle : 0.682 11.653 10346 Z= 0.338 Chirality : 0.043 0.260 1183 Planarity : 0.004 0.065 1236 Dihedral : 13.084 177.670 1256 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 1.49 % Allowed : 23.33 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 900 helix: 0.48 (0.24), residues: 461 sheet: -2.10 (0.54), residues: 91 loop : -3.14 (0.31), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 123 average time/residue: 0.1890 time to fit residues: 32.0061 Evaluate side-chains 111 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0780 time to fit residues: 1.7097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7573 Z= 0.230 Angle : 0.707 10.320 10346 Z= 0.354 Chirality : 0.045 0.230 1183 Planarity : 0.004 0.068 1236 Dihedral : 13.135 179.342 1256 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.82 % Allowed : 22.14 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 900 helix: 0.35 (0.24), residues: 462 sheet: -2.14 (0.54), residues: 94 loop : -3.05 (0.31), residues: 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 122 average time/residue: 0.1779 time to fit residues: 30.5244 Evaluate side-chains 121 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0727 time to fit residues: 2.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7573 Z= 0.268 Angle : 0.751 9.813 10346 Z= 0.379 Chirality : 0.047 0.262 1183 Planarity : 0.005 0.080 1236 Dihedral : 13.175 179.913 1256 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.45 % Allowed : 24.07 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.28), residues: 900 helix: 0.19 (0.24), residues: 459 sheet: -2.22 (0.54), residues: 95 loop : -3.07 (0.32), residues: 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 117 average time/residue: 0.1861 time to fit residues: 30.7640 Evaluate side-chains 112 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0712 time to fit residues: 1.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.0170 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 56 optimal weight: 0.0030 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7573 Z= 0.180 Angle : 0.710 11.551 10346 Z= 0.354 Chirality : 0.043 0.234 1183 Planarity : 0.004 0.078 1236 Dihedral : 13.037 177.693 1256 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.30 % Allowed : 25.11 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.28), residues: 900 helix: 0.35 (0.24), residues: 457 sheet: -2.08 (0.55), residues: 89 loop : -2.88 (0.32), residues: 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 120 average time/residue: 0.1878 time to fit residues: 31.2582 Evaluate side-chains 115 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1065 time to fit residues: 1.3144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.136979 restraints weight = 15824.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.140302 restraints weight = 9470.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.142577 restraints weight = 6635.867| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7573 Z= 0.269 Angle : 0.753 12.078 10346 Z= 0.380 Chirality : 0.046 0.260 1183 Planarity : 0.005 0.079 1236 Dihedral : 13.141 179.547 1256 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.74 % Allowed : 24.37 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.28), residues: 900 helix: 0.12 (0.24), residues: 463 sheet: -2.08 (0.55), residues: 93 loop : -3.05 (0.31), residues: 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.18 seconds wall clock time: 30 minutes 36.51 seconds (1836.51 seconds total)