Starting phenix.real_space_refine on Mon Mar 11 04:16:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/03_2024/8gh8_40036.pdb" } resolution = 4.3 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= 0.001 sd= 0.063 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 136 5.49 5 S 4 5.16 5 C 4084 2.51 5 N 1216 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 6991 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "B" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1044 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "C" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "D" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1053 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131} Chain: "E" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 4.14, per 1000 atoms: 0.59 Number of scatterers: 6991 At special positions: 0 Unit cell: (164.35, 167.2, 69.35, 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 4 16.00 P 136 15.00 O 1551 8.00 N 1216 7.00 C 4084 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: 3.16 Conformation dependent library (CDL) restraints added in 800.6 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 23.4% alpha, 5.2% beta 16 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.558A pdb=" N GLN A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 124 through 129 removed outlier: 4.400A pdb=" N LYS A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 129' Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.910A pdb=" N LEU B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.978A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.507A pdb=" N GLY B 129 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 removed outlier: 3.630A pdb=" N GLN C 36 " --> pdb=" O PRO C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.936A pdb=" N PHE C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 removed outlier: 3.856A pdb=" N ALA C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 86 " --> pdb=" O PRO C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 86' Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.936A pdb=" N LYS C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 67 through 75 removed outlier: 3.788A pdb=" N PHE D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.788A pdb=" N THR D 110 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.906A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.602A pdb=" N PHE B 26 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 27 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 20 removed outlier: 3.619A pdb=" N LEU C 59 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 29 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.675A pdb=" N GLY D 7 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 44 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 17 through 19 removed outlier: 5.622A pdb=" N PHE D 27 " --> pdb=" O LEU D 59 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1417 1.33 - 1.45: 2040 1.45 - 1.57: 3666 1.57 - 1.68: 268 1.68 - 1.80: 8 Bond restraints: 7399 Sorted by residual: bond pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.32e+01 bond pdb=" N LEU B 89 " pdb=" CA LEU B 89 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" N SER C 90 " pdb=" CA SER C 90 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 bond pdb=" C PRO C 132 " pdb=" N PRO C 133 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.12e-02 7.97e+03 9.08e+00 bond pdb=" N ALA C 91 " pdb=" CA ALA C 91 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.31e-02 5.83e+03 8.89e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.43: 955 106.43 - 113.21: 3901 113.21 - 119.98: 2568 119.98 - 126.75: 2689 126.75 - 133.52: 472 Bond angle restraints: 10585 Sorted by residual: angle pdb=" N SER B 90 " pdb=" CA SER B 90 " pdb=" C SER B 90 " ideal model delta sigma weight residual 113.18 103.04 10.14 1.21e+00 6.83e-01 7.03e+01 angle pdb=" C GLU D 66 " pdb=" CA GLU D 66 " pdb=" CB GLU D 66 " ideal model delta sigma weight residual 116.34 110.40 5.94 1.40e+00 5.10e-01 1.80e+01 angle pdb=" O LEU C 89 " pdb=" C LEU C 89 " pdb=" N SER C 90 " ideal model delta sigma weight residual 121.79 117.64 4.15 9.80e-01 1.04e+00 1.79e+01 angle pdb=" N ALA C 91 " pdb=" CA ALA C 91 " pdb=" C ALA C 91 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" CA ALA B 91 " pdb=" C ALA B 91 " pdb=" O ALA B 91 " ideal model delta sigma weight residual 120.51 115.14 5.37 1.43e+00 4.89e-01 1.41e+01 ... (remaining 10580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 3523 34.99 - 69.97: 580 69.97 - 104.96: 23 104.96 - 139.94: 1 139.94 - 174.93: 6 Dihedral angle restraints: 4133 sinusoidal: 2588 harmonic: 1545 Sorted by residual: dihedral pdb=" CA SER B 90 " pdb=" C SER B 90 " pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N GLY A 61 " pdb=" CA GLY A 61 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA PRO D 93 " pdb=" C PRO D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1208 0.113 - 0.226: 16 0.226 - 0.338: 0 0.338 - 0.451: 0 0.451 - 0.564: 3 Chirality restraints: 1227 Sorted by residual: chirality pdb=" P DG F 28 " pdb=" OP1 DG F 28 " pdb=" OP2 DG F 28 " pdb=" O5' DG F 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" P DA F 30 " pdb=" OP1 DA F 30 " pdb=" OP2 DA F 30 " pdb=" O5' DA F 30 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" P DA F 29 " pdb=" OP1 DA F 29 " pdb=" OP2 DA F 29 " pdb=" O5' DA F 29 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 1224 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 89 " -0.018 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LEU C 89 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C 89 " -0.021 2.00e-02 2.50e+03 pdb=" N SER C 90 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 93 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO D 94 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 93 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 94 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.032 5.00e-02 4.00e+02 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 835 2.76 - 3.29: 6239 3.29 - 3.83: 11306 3.83 - 4.36: 12441 4.36 - 4.90: 19026 Nonbonded interactions: 49847 Sorted by model distance: nonbonded pdb=" O ILE C 2 " pdb=" OG1 THR C 48 " model vdw 2.219 2.440 nonbonded pdb=" O ALA A 106 " pdb=" OG1 THR A 110 " model vdw 2.248 2.440 nonbonded pdb=" N LEU A 8 " pdb=" O LEU A 20 " model vdw 2.294 2.520 nonbonded pdb=" O LEU A 88 " pdb=" NH1 ARG A 117 " model vdw 2.323 2.520 nonbonded pdb=" NH2 ARG B 6 " pdb=" OE1 GLU B 43 " model vdw 2.327 2.520 ... (remaining 49842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 139) selection = chain 'B' selection = (chain 'C' and resid 1 through 139) selection = (chain 'D' and resid 1 through 139) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.890 Find NCS groups from input model: 0.360 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4247 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 0.047 7399 Z= 0.254 Angle : 0.791 10.142 10585 Z= 0.443 Chirality : 0.046 0.564 1227 Planarity : 0.006 0.068 871 Dihedral : 26.603 174.929 3151 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.70 % Favored : 86.75 % Rotamer: Outliers : 0.23 % Allowed : 0.00 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.65 (0.33), residues: 551 helix: -2.08 (0.62), residues: 70 sheet: -2.03 (1.10), residues: 18 loop : -2.78 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 49 PHE 0.021 0.002 PHE C 17 TYR 0.017 0.002 TYR A 60 ARG 0.006 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.509 Fit side-chains REVERT: B 12 LYS cc_start: 0.8310 (tttm) cc_final: 0.7868 (ttpt) REVERT: C 1 MET cc_start: 0.4402 (tpt) cc_final: 0.3078 (tpt) REVERT: D 1 MET cc_start: 0.4949 (tpt) cc_final: 0.3107 (tpt) outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.1991 time to fit residues: 15.9426 Evaluate side-chains 40 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4383 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7399 Z= 0.294 Angle : 0.749 11.918 10585 Z= 0.402 Chirality : 0.038 0.178 1227 Planarity : 0.006 0.069 871 Dihedral : 30.012 175.960 2143 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.79 % Favored : 85.84 % Rotamer: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.90 (0.32), residues: 551 helix: -2.25 (0.60), residues: 70 sheet: -2.23 (1.17), residues: 18 loop : -2.97 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 47 PHE 0.028 0.003 PHE C 62 TYR 0.019 0.003 TYR C 60 ARG 0.004 0.000 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.602 Fit side-chains REVERT: B 12 LYS cc_start: 0.8322 (tttm) cc_final: 0.7846 (ttpt) REVERT: C 1 MET cc_start: 0.4622 (tpt) cc_final: 0.3437 (tpt) REVERT: D 1 MET cc_start: 0.5309 (tpt) cc_final: 0.3544 (tpt) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1603 time to fit residues: 10.5417 Evaluate side-chains 38 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 0.0010 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4255 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7399 Z= 0.207 Angle : 0.701 11.368 10585 Z= 0.380 Chirality : 0.037 0.157 1227 Planarity : 0.005 0.062 871 Dihedral : 29.891 175.303 2143 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.62 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.72 (0.33), residues: 551 helix: -2.16 (0.62), residues: 69 sheet: -2.25 (0.91), residues: 24 loop : -2.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.017 0.002 PHE C 62 TYR 0.014 0.002 TYR A 60 ARG 0.005 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.578 Fit side-chains REVERT: B 12 LYS cc_start: 0.8282 (tttm) cc_final: 0.7866 (ttpt) REVERT: C 1 MET cc_start: 0.4706 (tpt) cc_final: 0.3573 (tpt) REVERT: D 1 MET cc_start: 0.5110 (tpt) cc_final: 0.3607 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1486 time to fit residues: 10.5860 Evaluate side-chains 43 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.0030 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 0.0870 chunk 53 optimal weight: 0.0040 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4267 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7399 Z= 0.209 Angle : 0.694 11.351 10585 Z= 0.375 Chirality : 0.037 0.179 1227 Planarity : 0.006 0.065 871 Dihedral : 29.766 175.294 2143 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.43 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.82 (0.33), residues: 551 helix: -2.03 (0.63), residues: 69 sheet: -3.49 (0.70), residues: 36 loop : -2.80 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 49 PHE 0.017 0.002 PHE C 17 TYR 0.014 0.002 TYR A 60 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.568 Fit side-chains REVERT: B 12 LYS cc_start: 0.8281 (tttm) cc_final: 0.7844 (ttpt) REVERT: C 1 MET cc_start: 0.4463 (tpt) cc_final: 0.3251 (tpt) REVERT: D 1 MET cc_start: 0.4911 (tpt) cc_final: 0.3430 (tpt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1484 time to fit residues: 10.9752 Evaluate side-chains 42 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4368 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7399 Z= 0.270 Angle : 0.729 11.631 10585 Z= 0.392 Chirality : 0.038 0.179 1227 Planarity : 0.006 0.067 871 Dihedral : 29.740 176.081 2143 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.70 % Favored : 85.12 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.78 (0.33), residues: 551 helix: -2.08 (0.62), residues: 70 sheet: -1.98 (1.21), residues: 18 loop : -2.90 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 49 PHE 0.022 0.003 PHE C 17 TYR 0.026 0.003 TYR D 60 ARG 0.006 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.523 Fit side-chains REVERT: B 12 LYS cc_start: 0.8365 (tttm) cc_final: 0.7861 (ttpt) REVERT: C 1 MET cc_start: 0.4777 (tpt) cc_final: 0.3522 (tpt) REVERT: D 1 MET cc_start: 0.4989 (tpt) cc_final: 0.3326 (tpt) REVERT: D 2 ILE cc_start: 0.6041 (mt) cc_final: 0.5095 (pt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1320 time to fit residues: 9.7335 Evaluate side-chains 42 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4309 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7399 Z= 0.222 Angle : 0.700 11.442 10585 Z= 0.379 Chirality : 0.037 0.167 1227 Planarity : 0.006 0.068 871 Dihedral : 29.668 175.775 2143 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.43 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.92 (0.33), residues: 551 helix: -2.24 (0.61), residues: 71 sheet: -3.47 (0.72), residues: 36 loop : -2.86 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 49 PHE 0.029 0.003 PHE C 26 TYR 0.017 0.002 TYR D 60 ARG 0.002 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.658 Fit side-chains REVERT: B 12 LYS cc_start: 0.8365 (tttm) cc_final: 0.7941 (ttpt) REVERT: C 1 MET cc_start: 0.4818 (tpt) cc_final: 0.3828 (tpt) REVERT: D 1 MET cc_start: 0.4803 (tpt) cc_final: 0.3284 (tpt) REVERT: D 2 ILE cc_start: 0.5829 (mt) cc_final: 0.4728 (pt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1316 time to fit residues: 9.3305 Evaluate side-chains 42 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.0170 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4241 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7399 Z= 0.196 Angle : 0.677 10.717 10585 Z= 0.366 Chirality : 0.036 0.157 1227 Planarity : 0.006 0.068 871 Dihedral : 29.561 175.357 2143 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.52 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.76 (0.33), residues: 551 helix: -2.15 (0.62), residues: 71 sheet: -2.32 (0.94), residues: 24 loop : -2.85 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 47 PHE 0.020 0.002 PHE D 17 TYR 0.011 0.001 TYR A 60 ARG 0.002 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.566 Fit side-chains REVERT: B 12 LYS cc_start: 0.8289 (tttm) cc_final: 0.7866 (ttpt) REVERT: C 1 MET cc_start: 0.4305 (tpt) cc_final: 0.3321 (tpt) REVERT: D 1 MET cc_start: 0.4688 (tpt) cc_final: 0.3310 (tpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1365 time to fit residues: 9.0201 Evaluate side-chains 39 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4353 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7399 Z= 0.255 Angle : 0.722 11.081 10585 Z= 0.384 Chirality : 0.038 0.163 1227 Planarity : 0.006 0.070 871 Dihedral : 29.554 176.365 2143 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.88 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.99 (0.33), residues: 551 helix: -2.16 (0.62), residues: 71 sheet: -3.55 (0.73), residues: 36 loop : -2.93 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.036 0.003 PHE C 26 TYR 0.014 0.002 TYR D 60 ARG 0.004 0.000 ARG D 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.567 Fit side-chains REVERT: B 12 LYS cc_start: 0.8345 (tttm) cc_final: 0.7880 (ttpt) REVERT: C 1 MET cc_start: 0.4504 (tpt) cc_final: 0.3220 (tpt) REVERT: C 48 THR cc_start: 0.4867 (p) cc_final: 0.4623 (p) REVERT: D 1 MET cc_start: 0.5161 (tpt) cc_final: 0.3467 (tpt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1356 time to fit residues: 9.5112 Evaluate side-chains 42 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 0.0010 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.0070 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 overall best weight: 1.7408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4459 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7399 Z= 0.330 Angle : 0.802 12.009 10585 Z= 0.419 Chirality : 0.040 0.177 1227 Planarity : 0.006 0.065 871 Dihedral : 29.556 177.240 2143 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.15 % Favored : 83.67 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.16 (0.32), residues: 551 helix: -2.25 (0.63), residues: 70 sheet: -2.39 (0.94), residues: 30 loop : -3.20 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 47 PHE 0.055 0.004 PHE C 26 TYR 0.014 0.003 TYR A 60 ARG 0.005 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.543 Fit side-chains REVERT: B 12 LYS cc_start: 0.8354 (tttm) cc_final: 0.7890 (ttpt) REVERT: C 1 MET cc_start: 0.4629 (tpt) cc_final: 0.3330 (tpt) REVERT: C 60 TYR cc_start: 0.4005 (m-80) cc_final: 0.3755 (m-80) REVERT: D 1 MET cc_start: 0.5251 (tpt) cc_final: 0.3524 (tpt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1651 time to fit residues: 11.0868 Evaluate side-chains 40 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4359 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7399 Z= 0.233 Angle : 0.726 11.567 10585 Z= 0.385 Chirality : 0.037 0.166 1227 Planarity : 0.006 0.066 871 Dihedral : 29.484 176.246 2143 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.52 % Favored : 85.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.11 (0.33), residues: 551 helix: -2.19 (0.62), residues: 71 sheet: -3.34 (0.78), residues: 36 loop : -3.06 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.031 0.003 PHE C 26 TYR 0.012 0.002 TYR D 60 ARG 0.013 0.001 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.570 Fit side-chains REVERT: B 12 LYS cc_start: 0.8360 (tttm) cc_final: 0.7802 (ttpp) REVERT: C 1 MET cc_start: 0.4533 (tpt) cc_final: 0.3636 (tpt) REVERT: D 1 MET cc_start: 0.4884 (tpt) cc_final: 0.3267 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1406 time to fit residues: 9.6905 Evaluate side-chains 38 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.0040 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.317570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.278187 restraints weight = 81521.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.281778 restraints weight = 36474.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.281217 restraints weight = 30629.332| |-----------------------------------------------------------------------------| r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4631 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7399 Z= 0.192 Angle : 0.679 10.604 10585 Z= 0.364 Chirality : 0.036 0.151 1227 Planarity : 0.006 0.065 871 Dihedral : 29.381 175.076 2143 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.87 (0.33), residues: 551 helix: -2.06 (0.63), residues: 70 sheet: -2.34 (0.98), residues: 24 loop : -2.96 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.018 0.002 PHE C 26 TYR 0.008 0.001 TYR A 60 ARG 0.006 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1395.87 seconds wall clock time: 25 minutes 54.98 seconds (1554.98 seconds total)