Starting phenix.real_space_refine on Thu Nov 14 17:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/11_2024/8gh8_40036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/11_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_40036/11_2024/8gh8_40036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/11_2024/8gh8_40036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/11_2024/8gh8_40036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh8_40036/11_2024/8gh8_40036.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.64, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 738.4 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: 2.54 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: 1.54 Time building geometry restraints manager: 1.95 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: 0.00 - 2.03: 10199 2.03 - 4.06: 335 4.06 - 6.09: 39 6.09 - 8.11: 10 8.11 - 10.14: 2 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 3.040 nonbonded pdb=" O ALA A 106 " pdb=" OG1 THR A 110 " model vdw 2.248 3.040 nonbonded pdb=" N LEU A 8 " pdb=" O LEU A 20 " model vdw 2.294 3.120 nonbonded pdb=" O LEU A 88 " pdb=" NH1 ARG A 117 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG B 6 " pdb=" OE1 GLU B 43 " model vdw 2.327 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.890 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.420 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: 0.2018 time to fit residues: 16.1219 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 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: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.4309 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7399 Z= 0.250 Angle : 0.726 11.999 10585 Z= 0.392 Chirality : 0.038 0.167 1227 Planarity : 0.006 0.069 871 Dihedral : 30.008 175.583 2143 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.89 % Favored : 88.75 % Rotamer: Outliers : 0.23 % Allowed : 8.35 % Favored : 91.42 % 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: -3.77 (0.32), residues: 551 helix: -2.22 (0.60), residues: 69 sheet: -3.04 (1.97), residues: 6 loop : -2.85 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 49 PHE 0.020 0.003 PHE C 62 TYR 0.019 0.003 TYR C 60 ARG 0.004 0.000 ARG A 117 *********************** 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 46 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.547 Fit side-chains REVERT: B 12 LYS cc_start: 0.8293 (tttm) cc_final: 0.7849 (ttpt) REVERT: C 1 MET cc_start: 0.4973 (tpt) cc_final: 0.3774 (tpt) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1445 time to fit residues: 9.9072 Evaluate side-chains 38 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.4292 moved from start: 0.1411 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= 0.232 Angle : 0.716 11.282 10585 Z= 0.387 Chirality : 0.038 0.185 1227 Planarity : 0.006 0.066 871 Dihedral : 29.891 175.453 2143 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.25 % Favored : 88.38 % 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: -3.80 (0.33), residues: 551 helix: -2.22 (0.62), residues: 69 sheet: -2.56 (0.88), residues: 24 loop : -2.85 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 49 PHE 0.018 0.002 PHE C 17 TYR 0.014 0.002 TYR A 60 ARG 0.006 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 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.563 Fit side-chains REVERT: B 12 LYS cc_start: 0.8268 (tttm) cc_final: 0.7863 (ttpt) REVERT: C 1 MET cc_start: 0.4975 (tpt) cc_final: 0.3616 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1387 time to fit residues: 9.4093 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 0.0000 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- 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: 0.4476 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7399 Z= 0.359 Angle : 0.830 11.739 10585 Z= 0.434 Chirality : 0.042 0.208 1227 Planarity : 0.006 0.066 871 Dihedral : 29.887 177.051 2143 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.88 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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: -4.08 (0.32), residues: 551 helix: -2.16 (0.63), residues: 69 sheet: -2.65 (0.89), residues: 30 loop : -3.11 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 47 PHE 0.030 0.004 PHE C 17 TYR 0.018 0.004 TYR A 60 ARG 0.005 0.001 ARG D 6 *********************** 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 48 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.520 Fit side-chains REVERT: B 12 LYS cc_start: 0.8313 (tttm) cc_final: 0.7893 (ttpt) REVERT: C 1 MET cc_start: 0.5318 (tpt) cc_final: 0.3999 (tpt) REVERT: C 95 ARG cc_start: 0.6379 (mmt180) cc_final: 0.3429 (tpm170) REVERT: D 1 MET cc_start: 0.5175 (tpt) cc_final: 0.3060 (tpt) REVERT: D 2 ILE cc_start: 0.6113 (mt) cc_final: 0.5062 (pt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1816 time to fit residues: 12.3582 Evaluate side-chains 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.0170 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4278 moved from start: 0.2115 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= 0.205 Angle : 0.718 11.792 10585 Z= 0.387 Chirality : 0.038 0.171 1227 Planarity : 0.006 0.066 871 Dihedral : 29.770 175.565 2143 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.98 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -3.80 (0.33), residues: 551 helix: -2.14 (0.63), residues: 69 sheet: -2.26 (1.12), residues: 16 loop : -2.89 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 49 PHE 0.022 0.002 PHE C 62 TYR 0.017 0.002 TYR D 60 ARG 0.003 0.000 ARG D 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 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.553 Fit side-chains REVERT: B 12 LYS cc_start: 0.8398 (tttm) cc_final: 0.7953 (ttpt) REVERT: C 1 MET cc_start: 0.5188 (tpt) cc_final: 0.3766 (tpt) REVERT: D 1 MET cc_start: 0.4806 (tpt) cc_final: 0.3306 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1353 time to fit residues: 9.3651 Evaluate side-chains 37 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.4331 moved from start: 0.2333 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= 0.229 Angle : 0.718 12.251 10585 Z= 0.386 Chirality : 0.037 0.165 1227 Planarity : 0.006 0.067 871 Dihedral : 29.708 175.838 2143 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.61 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -3.83 (0.33), residues: 551 helix: -2.21 (0.62), residues: 71 sheet: -2.27 (1.15), residues: 16 loop : -2.91 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 47 PHE 0.025 0.003 PHE C 26 TYR 0.018 0.002 TYR D 60 ARG 0.003 0.000 ARG D 99 *********************** 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 44 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.444 Fit side-chains REVERT: B 12 LYS cc_start: 0.8400 (tttm) cc_final: 0.7909 (ttpt) REVERT: C 1 MET cc_start: 0.5064 (tpt) cc_final: 0.3703 (tpt) REVERT: D 1 MET cc_start: 0.4980 (tpt) cc_final: 0.3501 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1476 time to fit residues: 9.9602 Evaluate side-chains 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 40 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 25 optimal weight: 0.0470 chunk 38 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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: 0.4205 moved from start: 0.2531 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= 0.189 Angle : 0.687 11.227 10585 Z= 0.370 Chirality : 0.036 0.150 1227 Planarity : 0.006 0.066 871 Dihedral : 29.604 175.169 2143 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.25 % Favored : 88.57 % 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: -3.69 (0.33), residues: 551 helix: -2.08 (0.62), residues: 69 sheet: -2.94 (1.51), residues: 6 loop : -2.80 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 49 PHE 0.019 0.002 PHE C 26 TYR 0.021 0.002 TYR C 4 ARG 0.003 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 to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.516 Fit side-chains REVERT: B 12 LYS cc_start: 0.8343 (tttm) cc_final: 0.7863 (ttpt) REVERT: C 1 MET cc_start: 0.4606 (tpt) cc_final: 0.3707 (tpt) REVERT: D 1 MET cc_start: 0.4638 (tpt) cc_final: 0.3249 (tpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1376 time to fit residues: 9.0663 Evaluate side-chains 35 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 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: 1.9990 chunk 26 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.4341 moved from start: 0.2725 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= 0.253 Angle : 0.726 11.576 10585 Z= 0.386 Chirality : 0.037 0.161 1227 Planarity : 0.006 0.072 871 Dihedral : 29.588 176.106 2143 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.61 % Favored : 86.21 % 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: -3.85 (0.33), residues: 551 helix: -2.13 (0.63), residues: 71 sheet: -2.61 (0.89), residues: 24 loop : -2.91 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 47 PHE 0.034 0.003 PHE C 26 TYR 0.015 0.002 TYR D 60 ARG 0.004 0.000 ARG D 95 *********************** 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 41 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.402 Fit side-chains REVERT: B 12 LYS cc_start: 0.8362 (tttm) cc_final: 0.7879 (ttpt) REVERT: C 1 MET cc_start: 0.4824 (tpt) cc_final: 0.3392 (tpt) REVERT: D 1 MET cc_start: 0.5025 (tpt) cc_final: 0.3534 (tpt) REVERT: D 128 LYS cc_start: 0.5872 (ptpp) cc_final: 0.4098 (tptt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1114 time to fit residues: 6.9203 Evaluate side-chains 39 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.4401 moved from start: 0.3137 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= 0.270 Angle : 0.750 12.602 10585 Z= 0.397 Chirality : 0.038 0.168 1227 Planarity : 0.006 0.067 871 Dihedral : 29.523 176.661 2143 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.97 % Favored : 85.84 % 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: -4.02 (0.33), residues: 551 helix: -2.19 (0.63), residues: 70 sheet: -2.71 (0.92), residues: 24 loop : -3.05 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 47 PHE 0.036 0.003 PHE C 26 TYR 0.017 0.003 TYR C 4 ARG 0.003 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 45 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.608 Fit side-chains REVERT: B 12 LYS cc_start: 0.8382 (tttm) cc_final: 0.7828 (ttpp) REVERT: C 1 MET cc_start: 0.4827 (tpt) cc_final: 0.3651 (tpt) REVERT: D 1 MET cc_start: 0.5028 (tpt) cc_final: 0.3447 (tpt) REVERT: D 128 LYS cc_start: 0.5796 (ptpp) cc_final: 0.4110 (tptt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1599 time to fit residues: 10.7398 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.4313 moved from start: 0.3231 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= 0.214 Angle : 0.711 12.166 10585 Z= 0.379 Chirality : 0.037 0.170 1227 Planarity : 0.006 0.066 871 Dihedral : 29.448 175.833 2143 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.43 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % 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: -3.86 (0.33), residues: 551 helix: -2.07 (0.65), residues: 69 sheet: -2.65 (1.27), residues: 12 loop : -2.95 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 47 PHE 0.027 0.002 PHE C 26 TYR 0.016 0.002 TYR C 4 ARG 0.010 0.001 ARG A 118 ********************** 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 42 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.449 Fit side-chains REVERT: B 12 LYS cc_start: 0.8342 (tttm) cc_final: 0.7867 (ttpt) REVERT: C 1 MET cc_start: 0.4712 (tpt) cc_final: 0.3641 (tpt) REVERT: D 1 MET cc_start: 0.4654 (tpt) cc_final: 0.3191 (tpt) REVERT: D 128 LYS cc_start: 0.5702 (ptpp) cc_final: 0.4063 (tptt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1307 time to fit residues: 8.1491 Evaluate side-chains 40 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 0.0170 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.4030 ------------------------------------------------------------------------------- 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** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.317163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.277592 restraints weight = 81743.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.280906 restraints weight = 36587.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.280218 restraints weight = 30634.969| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 moved from start: 0.3380 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= 0.199 Angle : 0.692 11.931 10585 Z= 0.371 Chirality : 0.036 0.165 1227 Planarity : 0.006 0.067 871 Dihedral : 29.397 175.482 2143 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.80 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.80 (0.33), residues: 551 helix: -2.09 (0.65), residues: 69 sheet: -2.81 (1.26), residues: 12 loop : -2.89 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 49 PHE 0.019 0.002 PHE C 26 TYR 0.014 0.002 TYR C 4 ARG 0.003 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.40 seconds wall clock time: 34 minutes 19.50 seconds (2059.50 seconds total)