Starting phenix.real_space_refine on Sat Dec 9 17:38:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlb_36391/12_2023/8jlb_36391.pdb" } resolution = 2.36 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= 0.005 sd= 0.050 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 289 5.49 5 S 10 5.16 5 C 6540 2.51 5 N 2221 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 6.85, per 1000 atoms: 0.58 Number of scatterers: 11844 At special positions: 0 Unit cell: (117.66, 110.24, 116.6, 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 10 16.00 P 289 15.00 O 2784 8.00 N 2221 7.00 C 6540 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: 6.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.981A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.421A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.998A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.504A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.901A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.166A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.485A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.979A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.294A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 6.74 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: 2141 1.33 - 1.45: 4215 1.45 - 1.57: 5692 1.57 - 1.69: 577 1.69 - 1.81: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" N ARG A 129 " pdb=" CA ARG A 129 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 4.00e+00 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C ASN F 64 " pdb=" O ASN F 64 " ideal model delta sigma weight residual 1.236 1.249 -0.013 1.15e-02 7.56e+03 1.21e+00 bond pdb=" C LEU B 49 " pdb=" O LEU B 49 " ideal model delta sigma weight residual 1.235 1.250 -0.015 1.33e-02 5.65e+03 1.19e+00 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 97.95 - 104.88: 1199 104.88 - 111.81: 6718 111.81 - 118.74: 3397 118.74 - 125.67: 6046 125.67 - 132.60: 961 Bond angle restraints: 18321 Sorted by residual: angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.34 117.97 -6.63 1.82e+00 3.02e-01 1.33e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.34 117.74 -6.40 1.82e+00 3.02e-01 1.24e+01 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 121.73 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" O ARG A 129 " ideal model delta sigma weight residual 120.90 117.88 3.02 1.07e+00 8.73e-01 7.96e+00 angle pdb=" CA MET D 59 " pdb=" CB MET D 59 " pdb=" CG MET D 59 " ideal model delta sigma weight residual 114.10 119.11 -5.01 2.00e+00 2.50e-01 6.29e+00 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 4319 21.34 - 42.68: 1358 42.68 - 64.02: 1117 64.02 - 85.37: 51 85.37 - 106.71: 4 Dihedral angle restraints: 6849 sinusoidal: 4697 harmonic: 2152 Sorted by residual: dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 55.63 -55.63 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.86 44.86 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.79 44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1338 0.034 - 0.068: 498 0.068 - 0.102: 190 0.102 - 0.136: 50 0.136 - 0.171: 7 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA ARG A 129 " pdb=" N ARG A 129 " pdb=" C ARG A 129 " pdb=" CB ARG A 129 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.903 9.50e-02 1.11e+02 4.05e-01 9.94e+01 pdb=" NE ARG A 129 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.028 2.00e-02 2.50e+03 1.66e-02 6.19e+00 pdb=" N1 DC I 69 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.030 2.00e-02 2.50e+03 1.35e-02 5.46e+00 pdb=" N9 DG I 47 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 20 2.57 - 3.15: 8418 3.15 - 3.74: 21350 3.74 - 4.32: 30563 4.32 - 4.90: 43287 Nonbonded interactions: 103638 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 1.988 2.440 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.133 2.496 nonbonded pdb=" OG SER C 40 " pdb=" O SER D 87 " model vdw 2.215 2.440 nonbonded pdb=" OG SER H 36 " pdb=" ND2 ASN H 63 " model vdw 2.305 2.520 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.382 2.520 ... (remaining 103633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.300 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: 1.960 Check model and map are aligned: 0.320 Set scattering table: 0.110 Process input model: 42.380 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.037 12645 Z= 0.215 Angle : 0.693 9.028 18321 Z= 0.436 Chirality : 0.043 0.171 2083 Planarity : 0.012 0.405 1316 Dihedral : 29.909 106.706 5465 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 18.34 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 730 helix: 0.83 (0.20), residues: 534 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE A 84 TYR 0.019 0.002 TYR F 88 ARG 0.007 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 2.2417 time to fit residues: 260.6261 Evaluate side-chains 102 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1476 time to fit residues: 1.3071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12645 Z= 0.399 Angle : 0.659 5.736 18321 Z= 0.399 Chirality : 0.042 0.129 2083 Planarity : 0.005 0.038 1316 Dihedral : 30.675 98.857 4003 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.62 % Allowed : 16.40 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.30), residues: 730 helix: 2.52 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 49 PHE 0.010 0.002 PHE D 70 TYR 0.022 0.002 TYR D 121 ARG 0.008 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 126 average time/residue: 2.2001 time to fit residues: 291.0579 Evaluate side-chains 121 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.0238 time to fit residues: 3.4302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12645 Z= 0.420 Angle : 0.652 9.780 18321 Z= 0.396 Chirality : 0.043 0.146 2083 Planarity : 0.005 0.043 1316 Dihedral : 30.325 89.567 4003 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 16.07 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.30), residues: 730 helix: 2.39 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.48 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 49 PHE 0.010 0.002 PHE D 70 TYR 0.016 0.002 TYR D 121 ARG 0.005 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.923 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 126 average time/residue: 2.1827 time to fit residues: 288.1827 Evaluate side-chains 127 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.4407 time to fit residues: 3.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12645 Z= 0.240 Angle : 0.613 9.212 18321 Z= 0.378 Chirality : 0.037 0.133 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.357 90.413 4003 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.30 % Allowed : 17.69 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.30), residues: 730 helix: 2.53 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.002 TYR D 121 ARG 0.007 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.852 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 127 average time/residue: 2.2236 time to fit residues: 295.7075 Evaluate side-chains 127 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.6046 time to fit residues: 3.1115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12645 Z= 0.395 Angle : 0.634 5.728 18321 Z= 0.387 Chirality : 0.041 0.160 2083 Planarity : 0.005 0.042 1316 Dihedral : 30.230 89.172 4003 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.11 % Allowed : 18.02 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.30), residues: 730 helix: 2.43 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.54 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.010 0.002 PHE D 70 TYR 0.012 0.002 TYR D 121 ARG 0.006 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 2.1006 time to fit residues: 273.1358 Evaluate side-chains 129 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.3396 time to fit residues: 4.1012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12645 Z= 0.187 Angle : 0.599 12.257 18321 Z= 0.369 Chirality : 0.035 0.129 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.300 90.487 4003 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.97 % Allowed : 19.32 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.31), residues: 730 helix: 2.70 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR D 40 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.949 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 126 average time/residue: 2.2244 time to fit residues: 293.5904 Evaluate side-chains 122 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1658 time to fit residues: 1.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12645 Z= 0.204 Angle : 0.583 6.147 18321 Z= 0.362 Chirality : 0.036 0.170 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.251 91.034 4003 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.81 % Allowed : 19.32 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.31), residues: 730 helix: 2.77 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE E 67 TYR 0.010 0.001 TYR D 40 ARG 0.002 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 2.1149 time to fit residues: 268.7397 Evaluate side-chains 125 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1258 time to fit residues: 1.4318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12645 Z= 0.238 Angle : 0.578 5.372 18321 Z= 0.359 Chirality : 0.036 0.133 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.199 90.565 4003 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.97 % Allowed : 19.64 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.31), residues: 730 helix: 2.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR D 40 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.968 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 127 average time/residue: 2.2240 time to fit residues: 296.5683 Evaluate side-chains 127 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.8600 time to fit residues: 2.9036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12645 Z= 0.280 Angle : 0.584 5.486 18321 Z= 0.361 Chirality : 0.037 0.139 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.104 89.684 4003 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.81 % Allowed : 19.97 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.30), residues: 730 helix: 2.77 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.002 TYR D 40 ARG 0.004 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.945 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 120 average time/residue: 2.2236 time to fit residues: 279.2661 Evaluate side-chains 121 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 3 average time/residue: 0.1337 time to fit residues: 1.7307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12645 Z= 0.202 Angle : 0.576 6.773 18321 Z= 0.358 Chirality : 0.035 0.129 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.110 89.853 4003 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 20.45 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.31), residues: 730 helix: 2.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR D 40 ARG 0.003 0.000 ARG G 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.975 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 120 average time/residue: 2.1729 time to fit residues: 273.4587 Evaluate side-chains 120 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1488 time to fit residues: 1.3445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103594 restraints weight = 15738.075| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.71 r_work: 0.3323 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12645 Z= 0.216 Angle : 0.575 6.555 18321 Z= 0.357 Chirality : 0.035 0.128 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.119 89.872 4003 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.49 % Allowed : 20.62 % Favored : 78.90 % 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: 3.04 (0.31), residues: 730 helix: 2.83 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.002 TYR F 88 ARG 0.003 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.43 seconds wall clock time: 82 minutes 37.21 seconds (4957.21 seconds total)