Starting phenix.real_space_refine on Thu Dec 7 20:06:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/12_2023/7yr6_34047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/12_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_34047/12_2023/7yr6_34047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/12_2023/7yr6_34047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/12_2023/7yr6_34047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/12_2023/7yr6_34047.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-1.21rc1-5172/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: 2.24, per 1000 atoms: 0.53 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: 1.66 Conformation dependent library (CDL) restraints added in 220.8 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: 1.45 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: 0.98 Time building geometry restraints manager: 1.79 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: 2457 35.86 - 71.71: 334 71.71 - 107.57: 49 107.57 - 143.42: 3 143.42 - 179.28: 2 Dihedral angle restraints: 2845 sinusoidal: 2227 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 2842 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: 0.520 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: 2.020 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- 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 : 25.596 179.280 2447 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 % Allowed : 12.09 % Favored : 84.62 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 43 TYR 0.008 0.001 TYR B 48 ARG 0.005 0.001 ARG C 44 *********************** 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 : 0.299 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: 0.2503 time to fit residues: 24.2646 Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0441 time to fit residues: 0.5414 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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** D 52 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7527 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4563 Z= 0.245 Angle : 0.667 6.363 6756 Z= 0.349 Chirality : 0.038 0.184 876 Planarity : 0.005 0.034 413 Dihedral : 26.499 179.418 2027 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Rotamer: Outliers : 0.55 % Allowed : 9.34 % Favored : 90.11 % 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 (0.49), residues: 212 helix: -2.58 (0.89), residues: 28 sheet: -2.95 (1.09), residues: 22 loop : -3.95 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 43 TYR 0.004 0.001 TYR E 48 ARG 0.008 0.001 ARG D 31 *********************** 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 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2578 time to fit residues: 17.1341 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3269 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4563 Z= 0.297 Angle : 0.753 6.746 6756 Z= 0.390 Chirality : 0.043 0.317 876 Planarity : 0.005 0.038 413 Dihedral : 26.856 175.986 2027 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 39.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Rotamer: Outliers : 0.55 % Allowed : 18.13 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.16 (0.49), residues: 212 helix: -2.43 (0.84), residues: 28 sheet: -3.09 (1.05), residues: 22 loop : -4.04 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS B 43 TYR 0.003 0.001 TYR C 48 ARG 0.004 0.001 ARG C 6 *********************** 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: 1 poor density : 57 time to evaluate : 0.237 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: 0 residues processed: 57 average time/residue: 0.2563 time to fit residues: 16.8953 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2885 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4563 Z= 0.262 Angle : 0.717 6.420 6756 Z= 0.377 Chirality : 0.041 0.220 876 Planarity : 0.005 0.029 413 Dihedral : 26.958 175.097 2027 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 37.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.55 % Allowed : 8.24 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.10 (0.50), residues: 212 helix: -2.24 (0.86), residues: 28 sheet: -3.26 (0.98), residues: 22 loop : -3.99 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS B 43 TYR 0.018 0.003 TYR B 48 ARG 0.007 0.001 ARG C 6 *********************** 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 54 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.328 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: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2507 time to fit residues: 15.9450 Evaluate side-chains 45 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2937 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 4563 Z= 0.448 Angle : 0.972 7.647 6756 Z= 0.502 Chirality : 0.052 0.341 876 Planarity : 0.007 0.037 413 Dihedral : 27.735 177.689 2027 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 61.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.94 % Favored : 74.06 % Rotamer: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.56 (0.48), residues: 212 helix: -3.08 (0.68), residues: 28 sheet: -2.72 (1.39), residues: 12 loop : -4.32 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.006 HIS E 43 TYR 0.006 0.002 TYR C 48 ARG 0.007 0.001 ARG C 6 *********************** 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 : 0.299 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: 0 residues processed: 54 average time/residue: 0.2443 time to fit residues: 15.4927 Evaluate side-chains 44 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3364 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4563 Z= 0.187 Angle : 0.683 7.508 6756 Z= 0.362 Chirality : 0.041 0.262 876 Planarity : 0.004 0.019 413 Dihedral : 27.016 174.361 2027 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.45 % Favored : 82.55 % Rotamer: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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: -5.35 (0.48), residues: 212 helix: -3.91 (0.62), residues: 22 sheet: -3.38 (0.95), residues: 22 loop : -3.90 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 43 TYR 0.009 0.002 TYR D 48 ARG 0.007 0.001 ARG D 50 *********************** 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 61 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.315 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: 61 average time/residue: 0.2386 time to fit residues: 17.0931 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3277 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4563 Z= 0.199 Angle : 0.673 6.259 6756 Z= 0.356 Chirality : 0.040 0.249 876 Planarity : 0.004 0.018 413 Dihedral : 26.913 173.652 2027 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 33.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -5.33 (0.48), residues: 212 helix: -3.59 (0.74), residues: 22 sheet: -3.30 (0.95), residues: 22 loop : -3.94 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 43 TYR 0.015 0.002 TYR B 48 ARG 0.003 0.001 ARG C 44 *********************** 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 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.308 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: 0.2298 time to fit residues: 15.6429 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3207 ------------------------------------------------------------------------------- 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: 20.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 4563 Z= 0.424 Angle : 0.948 7.973 6756 Z= 0.493 Chirality : 0.051 0.304 876 Planarity : 0.007 0.039 413 Dihedral : 27.621 176.068 2027 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 58.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.89 % Favored : 73.11 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -5.56 (0.48), residues: 212 helix: -3.81 (0.71), residues: 22 sheet: -2.59 (1.42), residues: 12 loop : -4.21 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.006 HIS E 43 TYR 0.011 0.002 TYR D 48 ARG 0.007 0.001 ARG E 6 *********************** 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 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2367 time to fit residues: 15.2962 Evaluate side-chains 41 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3205 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4563 Z= 0.250 Angle : 0.748 6.247 6756 Z= 0.397 Chirality : 0.044 0.279 876 Planarity : 0.005 0.044 413 Dihedral : 27.199 174.473 2027 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.06 % Favored : 75.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.49 (0.48), residues: 212 helix: -3.71 (0.78), residues: 22 sheet: -3.27 (0.94), residues: 22 loop : -4.08 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS B 43 TYR 0.023 0.002 TYR B 48 ARG 0.004 0.001 ARG C 7 *********************** 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 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.294 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: 55 average time/residue: 0.2325 time to fit residues: 15.1138 Evaluate side-chains 43 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3331 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4563 Z= 0.242 Angle : 0.718 6.112 6756 Z= 0.379 Chirality : 0.043 0.239 876 Planarity : 0.005 0.048 413 Dihedral : 27.007 174.134 2027 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.37 (0.49), residues: 212 helix: -3.46 (0.88), residues: 22 sheet: -3.17 (0.95), residues: 22 loop : -4.03 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS B 43 TYR 0.008 0.002 TYR D 48 ARG 0.003 0.001 ARG C 44 ********************** 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 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.372 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: 52 average time/residue: 0.2544 time to fit residues: 15.6868 Evaluate side-chains 41 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3183 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 1 optimal weight: 0.4980 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.064869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050343 restraints weight = 40380.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051820 restraints weight = 23476.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052842 restraints weight = 16006.223| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4563 Z= 0.233 Angle : 0.715 6.578 6756 Z= 0.375 Chirality : 0.042 0.231 876 Planarity : 0.005 0.045 413 Dihedral : 26.939 173.782 2027 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -5.36 (0.50), residues: 212 helix: -3.65 (0.84), residues: 22 sheet: -3.16 (0.96), residues: 22 loop : -3.99 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 43 TYR 0.005 0.001 TYR B 48 ARG 0.004 0.001 ARG C 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1018.33 seconds wall clock time: 20 minutes 29.57 seconds (1229.57 seconds total)