Starting phenix.real_space_refine (version: dev) on Tue Apr 5 02:48:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4d_30076/04_2022/6m4d_30076.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10497 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 693 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 693 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2548 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2577 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 6.12, per 1000 atoms: 0.58 Number of scatterers: 10497 At special positions: 0 Unit cell: (131.04, 79.04, 114.4, 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 14 16.00 P 250 15.00 O 2470 8.00 N 1962 7.00 C 5801 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: 5.78 Conformation dependent library (CDL) restraints added in 934.8 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1272 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 75.1% alpha, 0.9% beta 123 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.723A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 47 through 75 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 381 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 6.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1934 1.33 - 1.45: 3674 1.45 - 1.57: 5056 1.57 - 1.68: 498 1.68 - 1.80: 24 Bond restraints: 11186 Sorted by residual: bond pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 1.600 1.639 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.85e+00 bond pdb=" C5' DG J 136 " pdb=" C4' DG J 136 " ideal model delta sigma weight residual 1.518 1.551 -0.033 2.00e-02 2.50e+03 2.66e+00 bond pdb=" C1' DC I 56 " pdb=" N1 DC I 56 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" C3' DT J 128 " pdb=" O3' DT J 128 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.59e+00 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 96.35 - 103.62: 636 103.62 - 110.90: 5407 110.90 - 118.17: 3772 118.17 - 125.44: 5541 125.44 - 132.72: 817 Bond angle restraints: 16173 Sorted by residual: angle pdb=" O3' DC J 135 " pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 104.00 117.91 -13.91 1.50e+00 4.44e-01 8.60e+01 angle pdb=" C3' DC J 135 " pdb=" O3' DC J 135 " pdb=" P DG J 136 " ideal model delta sigma weight residual 120.20 131.11 -10.91 1.50e+00 4.44e-01 5.29e+01 angle pdb=" P DG J 136 " pdb=" O5' DG J 136 " pdb=" C5' DG J 136 " ideal model delta sigma weight residual 120.00 125.98 -5.98 1.50e+00 4.44e-01 1.59e+01 angle pdb=" C3' DC I 111 " pdb=" C2' DC I 111 " pdb=" C1' DC I 111 " ideal model delta sigma weight residual 101.60 96.35 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C5' DG J 136 " pdb=" C4' DG J 136 " pdb=" O4' DG J 136 " ideal model delta sigma weight residual 109.40 114.50 -5.10 1.50e+00 4.44e-01 1.16e+01 ... (remaining 16168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 4483 34.98 - 69.96: 1295 69.96 - 104.94: 65 104.94 - 139.92: 7 139.92 - 174.90: 2 Dihedral angle restraints: 5852 sinusoidal: 3882 harmonic: 1970 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS D 34 " pdb=" C LYS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1609 0.069 - 0.138: 218 0.138 - 0.207: 19 0.207 - 0.276: 3 0.276 - 0.345: 1 Chirality restraints: 1850 Sorted by residual: chirality pdb=" C1' DT J 13 " pdb=" O4' DT J 13 " pdb=" C2' DT J 13 " pdb=" N1 DT J 13 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1' DG I 19 " pdb=" O4' DG I 19 " pdb=" C2' DG I 19 " pdb=" N9 DG I 19 " both_signs ideal model delta sigma weight residual False 2.42 2.17 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" P DG J 136 " pdb=" OP1 DG J 136 " pdb=" OP2 DG J 136 " pdb=" O5' DG J 136 " both_signs ideal model delta sigma weight residual True 2.35 -2.59 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1847 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 13 " -0.036 2.00e-02 2.50e+03 2.52e-02 1.91e+01 pdb=" N9 DG I 13 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG I 13 " -0.030 2.00e-02 2.50e+03 pdb=" N7 DG I 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 13 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 13 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG I 13 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 13 " 0.016 2.00e-02 2.50e+03 pdb=" N2 DG I 13 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I 13 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG I 13 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 14 " 0.026 2.00e-02 2.50e+03 2.54e-02 1.78e+01 pdb=" N9 DA J 14 " -0.068 2.00e-02 2.50e+03 pdb=" C8 DA J 14 " 0.040 2.00e-02 2.50e+03 pdb=" N7 DA J 14 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J 14 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA J 14 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA J 14 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 14 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 14 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 14 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 72 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA C 72 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA C 72 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 352 2.64 - 3.20: 10613 3.20 - 3.77: 22149 3.77 - 4.33: 26096 4.33 - 4.90: 35636 Nonbonded interactions: 94846 Sorted by model distance: nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DC I 82 " model vdw 2.074 2.520 nonbonded pdb=" OG SER C 73 " pdb=" O VAL C 78 " model vdw 2.085 2.440 nonbonded pdb=" OG SER G 73 " pdb=" O VAL G 78 " model vdw 2.087 2.440 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.099 2.496 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.154 2.520 ... (remaining 94841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 250 5.49 5 S 14 5.16 5 C 5801 2.51 5 N 1962 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.610 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: 4.230 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 33.900 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.007 0.051 11186 Z= 0.384 Angle : 0.836 13.910 16173 Z= 0.502 Chirality : 0.048 0.345 1850 Planarity : 0.005 0.068 1178 Dihedral : 31.384 174.897 4580 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % Rotamer Outliers : 0.71 % 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: -2.81 (0.26), residues: 666 helix: -1.35 (0.20), residues: 490 sheet: None (None), residues: 0 loop : -2.95 (0.34), residues: 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 218 average time/residue: 0.3010 time to fit residues: 84.2516 Evaluate side-chains 138 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0912 time to fit residues: 1.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11186 Z= 0.213 Angle : 0.703 8.402 16173 Z= 0.410 Chirality : 0.041 0.254 1850 Planarity : 0.005 0.065 1178 Dihedral : 34.902 172.751 3268 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer Outliers : 0.00 % 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: -0.08 (0.31), residues: 666 helix: 0.89 (0.22), residues: 496 sheet: None (None), residues: 0 loop : -2.94 (0.35), residues: 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2602 time to fit residues: 70.5842 Evaluate side-chains 149 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11186 Z= 0.271 Angle : 0.696 9.216 16173 Z= 0.406 Chirality : 0.040 0.248 1850 Planarity : 0.005 0.060 1178 Dihedral : 34.806 173.665 3268 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer Outliers : 0.35 % 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: 0.46 (0.31), residues: 666 helix: 1.27 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.94 (0.34), residues: 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.2471 time to fit residues: 60.2952 Evaluate side-chains 124 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 113 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11186 Z= 0.293 Angle : 0.707 8.172 16173 Z= 0.413 Chirality : 0.040 0.242 1850 Planarity : 0.005 0.057 1178 Dihedral : 34.818 173.731 3268 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.70 % Favored : 96.70 % Rotamer Outliers : 0.00 % 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: 0.44 (0.31), residues: 666 helix: 1.28 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -2.86 (0.35), residues: 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2555 time to fit residues: 55.6332 Evaluate side-chains 122 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11186 Z= 0.279 Angle : 0.691 7.695 16173 Z= 0.404 Chirality : 0.040 0.252 1850 Planarity : 0.005 0.059 1178 Dihedral : 34.804 174.400 3268 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer Outliers : 0.18 % 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: 0.67 (0.32), residues: 666 helix: 1.48 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.82 (0.35), residues: 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2339 time to fit residues: 54.2973 Evaluate side-chains 119 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 63 ASN E 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 11186 Z= 0.210 Angle : 0.663 8.090 16173 Z= 0.385 Chirality : 0.039 0.268 1850 Planarity : 0.005 0.062 1178 Dihedral : 34.679 174.626 3268 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer Outliers : 0.00 % 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: 0.64 (0.32), residues: 666 helix: 1.36 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2381 time to fit residues: 58.2399 Evaluate side-chains 128 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 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 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11186 Z= 0.197 Angle : 0.652 8.162 16173 Z= 0.376 Chirality : 0.038 0.264 1850 Planarity : 0.005 0.063 1178 Dihedral : 34.504 173.186 3268 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer Outliers : 0.00 % 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: 0.89 (0.32), residues: 666 helix: 1.56 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.46 (0.38), residues: 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2368 time to fit residues: 60.3045 Evaluate side-chains 134 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11186 Z= 0.307 Angle : 0.707 8.010 16173 Z= 0.409 Chirality : 0.040 0.261 1850 Planarity : 0.005 0.062 1178 Dihedral : 34.652 172.176 3268 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.00 % Favored : 96.40 % Rotamer Outliers : 0.00 % 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: 0.28 (0.31), residues: 666 helix: 1.07 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -2.83 (0.37), residues: 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2364 time to fit residues: 54.0350 Evaluate side-chains 122 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.082 11186 Z= 0.485 Angle : 0.845 12.172 16173 Z= 0.484 Chirality : 0.046 0.267 1850 Planarity : 0.007 0.075 1178 Dihedral : 34.980 173.626 3268 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.60 % Favored : 95.80 % Rotamer Outliers : 0.00 % 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: -0.53 (0.30), residues: 666 helix: 0.49 (0.21), residues: 512 sheet: None (None), residues: 0 loop : -3.14 (0.34), residues: 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2666 time to fit residues: 49.8515 Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11186 Z= 0.233 Angle : 0.718 8.343 16173 Z= 0.411 Chirality : 0.040 0.218 1850 Planarity : 0.006 0.065 1178 Dihedral : 34.777 175.868 3268 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer Outliers : 0.00 % 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: -0.12 (0.31), residues: 666 helix: 0.77 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.88 (0.37), residues: 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2278 time to fit residues: 51.7606 Evaluate side-chains 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037876 restraints weight = 83498.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039050 restraints weight = 46773.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039854 restraints weight = 31666.838| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11186 Z= 0.217 Angle : 0.692 9.444 16173 Z= 0.396 Chirality : 0.039 0.234 1850 Planarity : 0.005 0.068 1178 Dihedral : 34.614 174.644 3268 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.40 % Favored : 97.15 % Rotamer Outliers : 0.00 % 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: 0.15 (0.32), residues: 666 helix: 0.98 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -2.86 (0.37), residues: 156 =============================================================================== Job complete usr+sys time: 1749.22 seconds wall clock time: 32 minutes 44.31 seconds (1964.31 seconds total)