Starting phenix.real_space_refine on Thu Dec 7 19:36:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7r_36046/12_2023/8j7r_36046.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 97 5.49 5 Mg 3 5.21 5 S 16 5.16 5 C 2154 2.51 5 N 721 2.21 5 O 1043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 859": "OE1" <-> "OE2" Residue "B GLU 870": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B GLU 968": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4034 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2083 Unusual residues: {' MG': 3} Classifications: {'RNA': 97, 'undetermined': 3, 'water': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p_pur': 43, 'rna3p_pyr': 41} Link IDs: {'rna2p': 13, 'rna3p': 83, None: 4} Not linked: pdbres=" C C 785 " pdbres=" MG C 801 " Not linked: pdbres=" MG C 801 " pdbres=" MG C 802 " Not linked: pdbres=" MG C 802 " pdbres=" MG C 803 " Not linked: pdbres=" MG C 803 " pdbres="HOH C 901 " Chain breaks: 2 Time building chain proxies: 3.03, per 1000 atoms: 0.75 Number of scatterers: 4034 At special positions: 0 Unit cell: (100.98, 91.8, 84.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 97 15.00 Mg 3 11.99 O 1043 8.00 N 721 7.00 C 2154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 396.2 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 85.7% alpha, 0.8% beta 37 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 754 through 771 removed outlier: 3.874A pdb=" N GLN B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.724A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.560A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.764A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.544A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.598A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 6.050A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.535A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'B' and resid 827 through 828 140 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 914 1.34 - 1.46: 1387 1.46 - 1.58: 1779 1.58 - 1.71: 191 1.71 - 1.83: 26 Bond restraints: 4297 Sorted by residual: bond pdb=" N ILE B 942 " pdb=" CA ILE B 942 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.90e+00 bond pdb=" N GLU B 852 " pdb=" CA GLU B 852 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.40e+00 bond pdb=" CA SER B 812 " pdb=" CB SER B 812 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.58e-02 4.01e+03 6.88e+00 bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.32e-02 5.74e+03 6.77e+00 bond pdb=" N LYS B 756 " pdb=" CA LYS B 756 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.21e+00 ... (remaining 4292 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.40: 459 105.40 - 112.63: 2459 112.63 - 119.85: 1982 119.85 - 127.08: 1120 127.08 - 134.30: 232 Bond angle restraints: 6252 Sorted by residual: angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 120.65 -6.95 1.50e+00 4.44e-01 2.15e+01 angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 118.40 -4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 102.60 98.18 4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" C3' U C 778 " pdb=" C2' U C 778 " pdb=" O2' U C 778 " ideal model delta sigma weight residual 110.70 116.85 -6.15 1.50e+00 4.44e-01 1.68e+01 angle pdb=" C4' U C 685 " pdb=" C3' U C 685 " pdb=" O3' U C 685 " ideal model delta sigma weight residual 113.00 107.18 5.82 1.50e+00 4.44e-01 1.50e+01 ... (remaining 6247 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 31.70: 2324 31.70 - 63.39: 287 63.39 - 95.08: 69 95.08 - 126.77: 2 126.77 - 158.46: 1 Dihedral angle restraints: 2683 sinusoidal: 1982 harmonic: 701 Sorted by residual: dihedral pdb=" C5' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" O3' A C 687 " ideal model delta sinusoidal sigma weight residual 147.00 109.30 37.70 1 8.00e+00 1.56e-02 3.13e+01 dihedral pdb=" O4' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" C2' A C 687 " ideal model delta sinusoidal sigma weight residual 24.00 -10.27 34.27 1 8.00e+00 1.56e-02 2.60e+01 dihedral pdb=" C3' A C 687 " pdb=" C4' A C 687 " pdb=" O4' A C 687 " pdb=" C1' A C 687 " ideal model delta sinusoidal sigma weight residual -2.00 29.65 -31.65 1 8.00e+00 1.56e-02 2.23e+01 ... (remaining 2680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 494 0.109 - 0.219: 206 0.219 - 0.328: 79 0.328 - 0.437: 0 0.437 - 0.546: 3 Chirality restraints: 782 Sorted by residual: chirality pdb=" P C C 751 " pdb=" OP1 C C 751 " pdb=" OP2 C C 751 " pdb=" O5' C C 751 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" P G C 682 " pdb=" OP1 G C 682 " pdb=" OP2 G C 682 " pdb=" O5' G C 682 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" P A C 760 " pdb=" OP1 A C 760 " pdb=" OP2 A C 760 " pdb=" O5' A C 760 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.85e+00 ... (remaining 779 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 839 " -0.023 2.00e-02 2.50e+03 1.62e-02 4.59e+00 pdb=" CG PHE B 839 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 839 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 839 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 839 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 839 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 839 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 704 " 0.029 2.00e-02 2.50e+03 1.19e-02 3.90e+00 pdb=" N9 A C 704 " -0.014 2.00e-02 2.50e+03 pdb=" C8 A C 704 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A C 704 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 704 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 704 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 704 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A C 704 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A C 704 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A C 704 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A C 704 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 685 " -0.023 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U C 685 " 0.025 2.00e-02 2.50e+03 pdb=" C2 U C 685 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U C 685 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 685 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U C 685 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U C 685 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U C 685 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U C 685 " 0.007 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 652 2.76 - 3.29: 3912 3.29 - 3.83: 8122 3.83 - 4.36: 9493 4.36 - 4.90: 12509 Nonbonded interactions: 34688 Sorted by model distance: nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.220 2.440 nonbonded pdb=" NZ LYS B 864 " pdb=" O LEU B 880 " model vdw 2.424 2.520 nonbonded pdb=" NE2 GLN B 980 " pdb=" OD1 ASP B 984 " model vdw 2.428 2.520 nonbonded pdb=" N GLU B 859 " pdb=" OE1 GLU B 859 " model vdw 2.444 2.520 nonbonded pdb=" OE1 GLU B 968 " pdb=" NZ LYS B 970 " model vdw 2.448 2.520 ... (remaining 34683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.770 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.010 0.041 4297 Z= 0.591 Angle : 1.340 6.949 6252 Z= 0.867 Chirality : 0.128 0.546 782 Planarity : 0.005 0.026 435 Dihedral : 23.754 158.465 2221 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.85 % Allowed : 23.29 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.53), residues: 236 helix: 0.49 (0.37), residues: 177 sheet: None (None), residues: 0 loop : -1.69 (0.81), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 990 HIS 0.007 0.004 HIS B 917 PHE 0.032 0.005 PHE B 839 TYR 0.010 0.002 TYR B 815 ARG 0.008 0.001 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.2272 time to fit residues: 23.0301 Evaluate side-chains 46 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1139 time to fit residues: 1.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 961 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4297 Z= 0.200 Angle : 0.599 8.276 6252 Z= 0.302 Chirality : 0.033 0.179 782 Planarity : 0.004 0.037 435 Dihedral : 22.754 162.097 1682 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 6.85 % Allowed : 28.31 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.56), residues: 236 helix: 1.49 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.21 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 990 HIS 0.001 0.001 HIS B 927 PHE 0.014 0.002 PHE B 959 TYR 0.007 0.002 TYR B 815 ARG 0.003 0.000 ARG B 820 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.358 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 55 average time/residue: 0.1544 time to fit residues: 10.7805 Evaluate side-chains 38 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0450 time to fit residues: 0.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 961 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4297 Z= 0.221 Angle : 0.583 6.411 6252 Z= 0.292 Chirality : 0.033 0.193 782 Planarity : 0.004 0.034 435 Dihedral : 22.370 159.456 1682 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.11 % Allowed : 33.79 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.56), residues: 236 helix: 1.91 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.97 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 990 HIS 0.001 0.001 HIS B 927 PHE 0.023 0.002 PHE B 959 TYR 0.005 0.002 TYR B 815 ARG 0.005 0.001 ARG B 954 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.280 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.1371 time to fit residues: 8.2484 Evaluate side-chains 34 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0412 time to fit residues: 0.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4297 Z= 0.259 Angle : 0.611 6.572 6252 Z= 0.303 Chirality : 0.034 0.194 782 Planarity : 0.004 0.030 435 Dihedral : 22.319 158.473 1682 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.65 % Allowed : 31.96 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.56), residues: 236 helix: 1.95 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.35 (1.11), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 990 HIS 0.001 0.000 HIS B 917 PHE 0.013 0.002 PHE B 959 TYR 0.022 0.004 TYR B 958 ARG 0.006 0.001 ARG B 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.269 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 37 average time/residue: 0.1307 time to fit residues: 6.6176 Evaluate side-chains 34 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0441 time to fit residues: 0.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4297 Z= 0.259 Angle : 0.600 6.529 6252 Z= 0.298 Chirality : 0.033 0.196 782 Planarity : 0.004 0.031 435 Dihedral : 22.240 157.845 1682 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.20 % Allowed : 33.33 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.56), residues: 236 helix: 1.99 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.42 (1.12), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.013 0.002 PHE B 959 TYR 0.009 0.002 TYR B 958 ARG 0.004 0.001 ARG B 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.345 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.1203 time to fit residues: 5.8377 Evaluate side-chains 30 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0457 time to fit residues: 0.6584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN B 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4297 Z= 0.165 Angle : 0.538 7.807 6252 Z= 0.264 Chirality : 0.030 0.181 782 Planarity : 0.003 0.031 435 Dihedral : 21.978 158.820 1682 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 34.70 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.56), residues: 236 helix: 2.39 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.34 (1.10), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 990 HIS 0.001 0.000 HIS B 917 PHE 0.010 0.001 PHE B 959 TYR 0.015 0.004 TYR B 958 ARG 0.004 0.000 ARG B 893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.332 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 32 average time/residue: 0.1455 time to fit residues: 6.2535 Evaluate side-chains 32 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.4822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4297 Z= 0.112 Angle : 0.491 7.911 6252 Z= 0.241 Chirality : 0.028 0.169 782 Planarity : 0.003 0.030 435 Dihedral : 21.759 158.863 1682 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.91 % Allowed : 35.16 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.55), residues: 236 helix: 2.80 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -0.31 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 990 HIS 0.001 0.000 HIS B 927 PHE 0.007 0.001 PHE B 839 TYR 0.011 0.003 TYR B 958 ARG 0.005 0.000 ARG B 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.328 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1421 time to fit residues: 7.3679 Evaluate side-chains 30 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0384 time to fit residues: 0.4095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 4297 Z= 0.444 Angle : 0.774 9.960 6252 Z= 0.381 Chirality : 0.039 0.224 782 Planarity : 0.005 0.029 435 Dihedral : 22.245 156.062 1682 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.65 % Allowed : 33.79 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.54), residues: 236 helix: 1.91 (0.36), residues: 196 sheet: None (None), residues: 0 loop : -1.31 (0.89), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP B 990 HIS 0.008 0.003 HIS B 917 PHE 0.019 0.002 PHE B 959 TYR 0.019 0.004 TYR B 958 ARG 0.005 0.001 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.327 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.1055 time to fit residues: 4.6667 Evaluate side-chains 29 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0473 time to fit residues: 0.7882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4297 Z= 0.212 Angle : 0.579 7.834 6252 Z= 0.292 Chirality : 0.032 0.194 782 Planarity : 0.003 0.027 435 Dihedral : 22.026 158.485 1682 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.91 % Allowed : 35.16 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.56), residues: 236 helix: 2.24 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -0.55 (0.99), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.012 0.002 PHE B 959 TYR 0.034 0.005 TYR B 958 ARG 0.004 0.000 ARG B 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.337 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1094 time to fit residues: 3.8675 Evaluate side-chains 24 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0446 time to fit residues: 0.4763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4297 Z= 0.199 Angle : 0.588 11.040 6252 Z= 0.290 Chirality : 0.031 0.192 782 Planarity : 0.003 0.028 435 Dihedral : 21.985 158.376 1682 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 36.07 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.56), residues: 236 helix: 2.31 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -0.58 (0.97), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.012 0.002 PHE B 959 TYR 0.032 0.005 TYR B 958 ARG 0.004 0.000 ARG B 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1154 time to fit residues: 3.7295 Evaluate side-chains 22 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** 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 = 0.3697 r_free = 0.3697 target = 0.106030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080671 restraints weight = 10046.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083031 restraints weight = 4894.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084586 restraints weight = 3321.606| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4297 Z= 0.127 Angle : 0.508 8.531 6252 Z= 0.256 Chirality : 0.029 0.176 782 Planarity : 0.003 0.030 435 Dihedral : 21.778 158.795 1682 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.46 % Allowed : 36.99 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.55), residues: 236 helix: 2.53 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.60 (0.97), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 990 HIS 0.001 0.000 HIS B 917 PHE 0.009 0.001 PHE B 776 TYR 0.026 0.004 TYR B 958 ARG 0.004 0.000 ARG B 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 764.70 seconds wall clock time: 14 minutes 49.76 seconds (889.76 seconds total)