Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 20:27:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/07_2023/7yr6_34047.pdb" } resolution = 4.8 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= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 8 5.16 5 C 2197 2.51 5 N 797 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 7": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 7, 'rna3p_pur': 52, 'rna3p_pyr': 39} Link IDs: {'rna2p': 26, 'rna3p': 91} Time building chain proxies: 2.63, per 1000 atoms: 0.62 Number of scatterers: 4248 At special positions: 0 Unit cell: (84.15, 91.8, 101.15, 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 8 16.00 P 118 15.00 O 1128 8.00 N 797 7.00 C 2197 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: 2.32 Conformation dependent library (CDL) restraints added in 272.8 milliseconds 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 398 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 3 sheets defined 14.1% alpha, 14.1% beta 30 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'B' and resid 45 through 49 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.787A pdb=" N GLY D 33 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 26 removed outlier: 5.104A pdb=" N VAL C 22 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 33 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 30 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 6 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.744A pdb=" N THR B 21 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 33 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 2.44 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: 672 1.33 - 1.45: 1678 1.45 - 1.57: 1962 1.57 - 1.69: 235 1.69 - 1.80: 16 Bond restraints: 4563 Sorted by residual: bond pdb=" O3' C A 15 " pdb=" P G A 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.50e-02 4.44e+03 1.54e+01 bond pdb=" O3' G A 57 " pdb=" P A A 58 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O3' C A 61 " pdb=" P C A 62 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.77e+00 bond pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" O3' A A 63 " pdb=" P U A 64 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.28e+00 ... (remaining 4558 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.06: 686 106.06 - 112.80: 2542 112.80 - 119.55: 1447 119.55 - 126.30: 1694 126.30 - 133.05: 387 Bond angle restraints: 6756 Sorted by residual: angle pdb=" O3' C A 61 " pdb=" C3' C A 61 " pdb=" C2' C A 61 " ideal model delta sigma weight residual 109.50 119.51 -10.01 1.50e+00 4.44e-01 4.46e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" C ILE E 47 " pdb=" N TYR E 48 " pdb=" CA TYR E 48 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" O3' G A 81 " pdb=" C3' G A 81 " pdb=" C2' G A 81 " ideal model delta sigma weight residual 109.50 115.96 -6.46 1.50e+00 4.44e-01 1.85e+01 angle pdb=" N LEU E 23 " pdb=" CA LEU E 23 " pdb=" C LEU E 23 " ideal model delta sigma weight residual 110.88 116.23 -5.35 1.28e+00 6.10e-01 1.75e+01 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 2275 35.86 - 71.71: 171 71.71 - 107.57: 20 107.57 - 143.42: 3 143.42 - 179.28: 2 Dihedral angle restraints: 2471 sinusoidal: 1853 harmonic: 618 Sorted by residual: dihedral pdb=" O4' U A 60 " pdb=" C1' U A 60 " pdb=" N1 U A 60 " pdb=" C2 U A 60 " ideal model delta sinusoidal sigma weight residual 200.00 53.25 146.75 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' G A 39 " pdb=" C1' G A 39 " pdb=" N9 G A 39 " pdb=" C4 G A 39 " ideal model delta sinusoidal sigma weight residual 68.00 153.16 -85.16 1 1.70e+01 3.46e-03 3.04e+01 dihedral pdb=" CA VAL D 18 " pdb=" C VAL D 18 " pdb=" N THR D 19 " pdb=" CA THR D 19 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 2468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 822 0.105 - 0.210: 46 0.210 - 0.316: 6 0.316 - 0.421: 1 0.421 - 0.526: 1 Chirality restraints: 876 Sorted by residual: chirality pdb=" C3' C A 61 " pdb=" C4' C A 61 " pdb=" O3' C A 61 " pdb=" C2' C A 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB ILE C 32 " pdb=" CA ILE C 32 " pdb=" CG1 ILE C 32 " pdb=" CG2 ILE C 32 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" P G A 57 " pdb=" OP1 G A 57 " pdb=" OP2 G A 57 " pdb=" O5' G A 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 873 not shown) Planarity restraints: 413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 35 " -0.022 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" N9 G A 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A 35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 91 " 0.021 2.00e-02 2.50e+03 1.08e-02 2.63e+00 pdb=" N1 U A 91 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U A 91 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 91 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 91 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U A 91 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 91 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 48 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C TYR E 48 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR E 48 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN E 49 " -0.009 2.00e-02 2.50e+03 ... (remaining 410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1060 2.81 - 3.33: 3678 3.33 - 3.86: 8638 3.86 - 4.38: 9229 4.38 - 4.90: 12472 Nonbonded interactions: 35077 Sorted by model distance: nonbonded pdb=" O2' G A 50 " pdb=" O4' G A 51 " model vdw 2.291 2.440 nonbonded pdb=" O2' A A 41 " pdb=" O5' G A 43 " model vdw 2.326 2.440 nonbonded pdb=" O GLU B 10 " pdb=" OG1 THR B 21 " model vdw 2.342 2.440 nonbonded pdb=" O VAL E 40 " pdb=" N1 G A 10 " model vdw 2.370 2.520 nonbonded pdb=" O VAL B 42 " pdb=" N2 G A 39 " model vdw 2.397 2.520 ... (remaining 35072 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 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) } 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: 0.510 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: 2.680 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.830 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 4563 Z= 0.260 Angle : 0.883 10.014 6756 Z= 0.497 Chirality : 0.055 0.526 876 Planarity : 0.004 0.028 413 Dihedral : 20.675 179.280 2073 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer Outliers : 3.30 % 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: -5.39 (0.42), residues: 212 helix: -3.34 (0.76), residues: 24 sheet: -3.13 (0.95), residues: 29 loop : -4.07 (0.34), residues: 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.330 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 outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.2590 time to fit residues: 25.0831 Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0430 time to fit residues: 0.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4563 Z= 0.146 Angle : 0.559 5.333 6756 Z= 0.297 Chirality : 0.035 0.169 876 Planarity : 0.004 0.028 413 Dihedral : 20.181 176.936 1653 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer Outliers : 0.55 % 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: -5.08 (0.46), residues: 212 helix: -2.71 (0.86), residues: 28 sheet: -2.80 (1.09), residues: 22 loop : -3.94 (0.39), residues: 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.307 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 outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.2595 time to fit residues: 19.5533 Evaluate side-chains 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0445 time to fit residues: 0.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 8.9990 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 4563 Z= 0.308 Angle : 0.747 8.133 6756 Z= 0.388 Chirality : 0.042 0.203 876 Planarity : 0.006 0.053 413 Dihedral : 21.413 176.079 1653 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 41.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.53 % Favored : 75.47 % Rotamer Outliers : 1.10 % 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: -5.19 (0.48), residues: 212 helix: -2.84 (0.78), residues: 28 sheet: -2.73 (1.07), residues: 22 loop : -4.03 (0.42), residues: 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.289 Fit side-chains 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: 57 average time/residue: 0.2491 time to fit residues: 16.5390 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4563 Z= 0.179 Angle : 0.613 6.054 6756 Z= 0.324 Chirality : 0.037 0.191 876 Planarity : 0.004 0.025 413 Dihedral : 21.040 174.679 1653 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % 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: -5.08 (0.48), residues: 212 helix: -2.97 (0.71), residues: 28 sheet: -2.56 (1.12), residues: 22 loop : -3.94 (0.42), residues: 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.311 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 outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2759 time to fit residues: 18.1502 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 overall best weight: 7.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 4563 Z= 0.421 Angle : 0.945 9.377 6756 Z= 0.485 Chirality : 0.051 0.259 876 Planarity : 0.007 0.052 413 Dihedral : 22.504 174.951 1653 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 58.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.42 % Favored : 73.58 % Rotamer Outliers : 0.55 % 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: -5.24 (0.50), residues: 212 helix: -3.07 (0.67), residues: 28 sheet: -2.89 (1.50), residues: 12 loop : -4.01 (0.44), residues: 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2329 time to fit residues: 15.1782 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0444 time to fit residues: 0.4027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4563 Z= 0.217 Angle : 0.676 6.337 6756 Z= 0.356 Chirality : 0.041 0.211 876 Planarity : 0.004 0.022 413 Dihedral : 21.787 173.572 1653 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % 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: -4.97 (0.50), residues: 212 helix: -2.72 (0.73), residues: 22 sheet: -2.73 (1.16), residues: 22 loop : -3.83 (0.43), residues: 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.294 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: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2457 time to fit residues: 17.2723 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4563 Z= 0.177 Angle : 0.643 6.936 6756 Z= 0.340 Chirality : 0.039 0.193 876 Planarity : 0.004 0.030 413 Dihedral : 21.422 172.517 1653 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.17 % Favored : 77.83 % 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: -4.98 (0.50), residues: 212 helix: -3.12 (0.74), residues: 22 sheet: -2.46 (1.26), residues: 22 loop : -3.83 (0.42), residues: 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.289 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: 59 average time/residue: 0.2234 time to fit residues: 15.6074 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 4563 Z= 0.436 Angle : 0.932 7.080 6756 Z= 0.482 Chirality : 0.051 0.247 876 Planarity : 0.006 0.038 413 Dihedral : 22.629 175.357 1653 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 59.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.36 % Favored : 72.64 % 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: -5.31 (0.50), residues: 212 helix: -3.43 (0.71), residues: 22 sheet: -3.02 (1.43), residues: 12 loop : -4.00 (0.43), residues: 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.280 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: 54 average time/residue: 0.2320 time to fit residues: 14.8588 Evaluate side-chains 43 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 10.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4563 Z= 0.248 Angle : 0.721 5.959 6756 Z= 0.379 Chirality : 0.042 0.251 876 Planarity : 0.004 0.024 413 Dihedral : 22.098 173.854 1653 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 38.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % 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: -5.27 (0.50), residues: 212 helix: -3.22 (0.77), residues: 22 sheet: -3.46 (0.98), residues: 22 loop : -3.92 (0.43), residues: 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.307 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: 58 average time/residue: 0.2370 time to fit residues: 16.1515 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 4563 Z= 0.309 Angle : 0.790 6.244 6756 Z= 0.415 Chirality : 0.045 0.251 876 Planarity : 0.006 0.052 413 Dihedral : 22.342 174.157 1653 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 44.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.89 % Favored : 73.11 % 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: -5.19 (0.50), residues: 212 helix: -3.25 (0.79), residues: 22 sheet: -3.14 (1.41), residues: 12 loop : -3.90 (0.43), residues: 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.325 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: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2141 time to fit residues: 13.5129 Evaluate side-chains 41 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047540 restraints weight = 37233.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049132 restraints weight = 21118.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.050261 restraints weight = 14185.918| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 4563 Z= 0.332 Angle : 0.825 7.462 6756 Z= 0.432 Chirality : 0.046 0.301 876 Planarity : 0.005 0.041 413 Dihedral : 22.545 174.851 1653 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 46.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.42 % Favored : 73.58 % 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: -5.23 (0.50), residues: 212 helix: -3.46 (0.79), residues: 22 sheet: -3.09 (1.39), residues: 12 loop : -3.91 (0.42), residues: 178 =============================================================================== Job complete usr+sys time: 990.18 seconds wall clock time: 18 minutes 40.68 seconds (1120.68 seconds total)