Starting phenix.real_space_refine on Fri Mar 15 18:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz5_21970/03_2024/6wz5_21970.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 306 5.49 5 S 12 5.16 5 C 6860 2.51 5 N 2349 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3155 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3118 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Time building chain proxies: 6.72, per 1000 atoms: 0.54 Number of scatterers: 12443 At special positions: 0 Unit cell: (74.2, 116.6, 122.96, 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 12 16.00 P 306 15.00 O 2916 8.00 N 2349 7.00 C 6860 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: 6.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 3.1% beta 153 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A 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 removed outlier: 3.743A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.335A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.987A 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 removed outlier: 3.706A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) 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: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.773A 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 removed outlier: 6.695A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.928A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.556A 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: 6.789A 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: 7.055A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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: 392 hydrogen bonds 780 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1867 1.32 - 1.44: 4639 1.44 - 1.56: 6148 1.56 - 1.68: 610 1.68 - 1.80: 22 Bond restraints: 13286 Sorted by residual: bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.339 1.251 0.088 5.57e-02 3.22e+02 2.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.379 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 ... (remaining 13281 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.16: 1338 105.16 - 112.01: 7340 112.01 - 118.86: 3357 118.86 - 125.71: 6226 125.71 - 132.56: 988 Bond angle restraints: 19249 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.95 -5.77 2.37e+00 1.78e-01 5.93e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.83 -3.63 1.50e+00 4.44e-01 5.84e+00 angle pdb=" C3' DC I -26 " pdb=" C2' DC I -26 " pdb=" C1' DC I -26 " ideal model delta sigma weight residual 101.60 98.31 3.29 1.50e+00 4.44e-01 4.82e+00 angle pdb=" C SER H 75 " pdb=" N ARG H 76 " pdb=" CA ARG H 76 " ideal model delta sigma weight residual 121.14 117.37 3.77 1.75e+00 3.27e-01 4.63e+00 angle pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " pdb=" C1' DC I -25 " ideal model delta sigma weight residual 101.60 98.43 3.17 1.50e+00 4.44e-01 4.46e+00 ... (remaining 19244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5548 33.12 - 66.24: 1634 66.24 - 99.36: 32 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 7216 sinusoidal: 4964 harmonic: 2252 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.87 139.13 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1149 0.030 - 0.060: 710 0.060 - 0.090: 252 0.090 - 0.119: 63 0.119 - 0.149: 18 Chirality restraints: 2192 Sorted by residual: chirality pdb=" C4' DA J -35 " pdb=" C5' DA J -35 " pdb=" O4' DA J -35 " pdb=" C3' DA J -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ARG H 76 " pdb=" N ARG H 76 " pdb=" C ARG H 76 " pdb=" CB ARG H 76 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C4' DA I 26 " pdb=" C5' DA I 26 " pdb=" O4' DA I 26 " pdb=" C3' DA I 26 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2189 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 43 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.026 2.00e-02 2.50e+03 1.19e-02 3.92e+00 pdb=" N9 DA I 26 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2451 2.78 - 3.31: 10584 3.31 - 3.84: 26079 3.84 - 4.37: 31295 4.37 - 4.90: 42128 Nonbonded interactions: 112537 Sorted by model distance: nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.253 2.520 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.260 2.440 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.320 2.520 nonbonded pdb=" N2 DG I 38 " pdb=" O2 DC J -38 " model vdw 2.329 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.366 2.440 ... (remaining 112532 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=1.00 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: 5.060 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: 24.680 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 41.590 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 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 : 0.008 0.088 13286 Z= 0.468 Angle : 0.693 8.565 19249 Z= 0.424 Chirality : 0.043 0.149 2192 Planarity : 0.005 0.051 1372 Dihedral : 28.628 165.601 5760 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 3.24 % Favored : 95.83 % 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: -0.00 (0.27), residues: 758 helix: 0.51 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE A 67 TYR 0.014 0.002 TYR G 57 ARG 0.006 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 0.972 Fit side-chains REVERT: G 15 LYS cc_start: 0.7464 (mtpp) cc_final: 0.7220 (mtpt) REVERT: G 24 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7781 (mm-40) REVERT: H 68 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6886 (mp0) outliers start: 6 outliers final: 2 residues processed: 196 average time/residue: 1.8812 time to fit residues: 388.7708 Evaluate side-chains 149 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 31 HIS C 104 GLN E 68 GLN G 24 GLN G 31 HIS G 110 ASN H 44 GLN H 92 GLN H 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13286 Z= 0.259 Angle : 0.649 8.114 19249 Z= 0.386 Chirality : 0.037 0.164 2192 Planarity : 0.005 0.051 1372 Dihedral : 31.337 161.885 4208 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.62 % Allowed : 13.89 % Favored : 83.49 % 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: 1.69 (0.28), residues: 758 helix: 1.79 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.68 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS A 39 PHE 0.010 0.002 PHE E 67 TYR 0.010 0.002 TYR E 41 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.025 Fit side-chains REVERT: C 15 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7760 (tttm) REVERT: H 29 THR cc_start: 0.7682 (t) cc_final: 0.7466 (p) outliers start: 17 outliers final: 0 residues processed: 187 average time/residue: 1.9632 time to fit residues: 386.2415 Evaluate side-chains 159 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13286 Z= 0.329 Angle : 0.636 7.750 19249 Z= 0.378 Chirality : 0.038 0.143 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.720 165.511 4202 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % 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: 2.12 (0.28), residues: 758 helix: 2.09 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.46 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 39 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.002 TYR G 57 ARG 0.008 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.004 Fit side-chains REVERT: A 42 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7957 (mtp85) REVERT: C 15 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7748 (ttmm) REVERT: D 54 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8622 (mmmt) REVERT: H 29 THR cc_start: 0.7801 (t) cc_final: 0.7550 (p) outliers start: 15 outliers final: 7 residues processed: 162 average time/residue: 2.2002 time to fit residues: 374.2807 Evaluate side-chains 158 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13286 Z= 0.333 Angle : 0.629 7.450 19249 Z= 0.375 Chirality : 0.038 0.140 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.513 169.454 4202 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.70 % Allowed : 14.66 % Favored : 83.64 % 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: 2.28 (0.29), residues: 758 helix: 2.20 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.002 TYR B 51 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.976 Fit side-chains REVERT: C 15 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7643 (ttmm) REVERT: H 29 THR cc_start: 0.8070 (t) cc_final: 0.7803 (p) outliers start: 11 outliers final: 7 residues processed: 154 average time/residue: 2.0970 time to fit residues: 338.9725 Evaluate side-chains 155 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13286 Z= 0.220 Angle : 0.598 7.978 19249 Z= 0.361 Chirality : 0.035 0.123 2192 Planarity : 0.004 0.050 1372 Dihedral : 31.539 169.624 4202 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.01 % Allowed : 14.04 % Favored : 83.95 % 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: 2.51 (0.29), residues: 758 helix: 2.37 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 39 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.545 Fit side-chains REVERT: C 15 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7625 (ttmm) REVERT: D 54 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8500 (mmmm) REVERT: G 73 ASN cc_start: 0.7855 (t0) cc_final: 0.7653 (t160) REVERT: H 29 THR cc_start: 0.8055 (t) cc_final: 0.7832 (p) REVERT: H 90 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7645 (mp0) outliers start: 13 outliers final: 7 residues processed: 153 average time/residue: 2.1477 time to fit residues: 344.7851 Evaluate side-chains 159 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13286 Z= 0.286 Angle : 0.604 7.576 19249 Z= 0.363 Chirality : 0.037 0.127 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.462 169.762 4202 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % 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: 2.57 (0.29), residues: 758 helix: 2.40 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.055 Fit side-chains REVERT: C 15 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7606 (ttmm) REVERT: D 56 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8485 (tpp) REVERT: G 73 ASN cc_start: 0.7944 (t0) cc_final: 0.7553 (t160) REVERT: H 29 THR cc_start: 0.8154 (t) cc_final: 0.7882 (p) outliers start: 8 outliers final: 6 residues processed: 148 average time/residue: 2.0386 time to fit residues: 316.9172 Evaluate side-chains 152 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13286 Z= 0.247 Angle : 0.596 7.767 19249 Z= 0.360 Chirality : 0.035 0.121 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.469 169.714 4202 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.23 % Allowed : 15.12 % Favored : 83.64 % 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: 2.62 (0.29), residues: 758 helix: 2.44 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 0.968 Fit side-chains REVERT: C 15 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7599 (ttmm) REVERT: G 73 ASN cc_start: 0.7938 (t0) cc_final: 0.7539 (t160) REVERT: H 29 THR cc_start: 0.8158 (t) cc_final: 0.7885 (p) outliers start: 8 outliers final: 6 residues processed: 147 average time/residue: 2.0637 time to fit residues: 318.8854 Evaluate side-chains 149 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.0170 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13286 Z= 0.281 Angle : 0.599 7.624 19249 Z= 0.360 Chirality : 0.036 0.125 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.449 169.914 4202 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.54 % Allowed : 14.66 % Favored : 83.80 % 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: 2.68 (0.29), residues: 758 helix: 2.52 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.803 Fit side-chains REVERT: C 15 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7595 (ttmm) REVERT: G 73 ASN cc_start: 0.7949 (t0) cc_final: 0.7511 (t160) REVERT: H 29 THR cc_start: 0.8177 (t) cc_final: 0.7898 (p) REVERT: H 90 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7571 (mp0) outliers start: 10 outliers final: 7 residues processed: 148 average time/residue: 2.0034 time to fit residues: 311.5707 Evaluate side-chains 153 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13286 Z= 0.267 Angle : 0.596 7.641 19249 Z= 0.359 Chirality : 0.036 0.123 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.449 169.952 4202 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 15.59 % Favored : 83.02 % 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: 2.69 (0.29), residues: 758 helix: 2.52 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 0.990 Fit side-chains REVERT: C 15 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7594 (ttmm) REVERT: G 73 ASN cc_start: 0.7943 (t0) cc_final: 0.7507 (t160) REVERT: H 29 THR cc_start: 0.8175 (t) cc_final: 0.7900 (p) REVERT: H 90 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7576 (mp0) outliers start: 9 outliers final: 7 residues processed: 146 average time/residue: 1.9464 time to fit residues: 298.3815 Evaluate side-chains 151 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0370 chunk 68 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13286 Z= 0.230 Angle : 0.593 7.866 19249 Z= 0.358 Chirality : 0.035 0.120 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.451 169.892 4202 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 15.59 % Favored : 83.02 % 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: 2.72 (0.29), residues: 758 helix: 2.55 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.003 0.000 ARG H 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.957 Fit side-chains REVERT: C 15 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7590 (ttmm) REVERT: G 73 ASN cc_start: 0.7938 (t0) cc_final: 0.7496 (t160) REVERT: H 29 THR cc_start: 0.8174 (t) cc_final: 0.7906 (p) REVERT: H 90 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7569 (mp0) outliers start: 9 outliers final: 7 residues processed: 149 average time/residue: 2.1109 time to fit residues: 329.8885 Evaluate side-chains 152 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082425 restraints weight = 16555.151| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.86 r_work: 0.3034 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13286 Z= 0.259 Angle : 0.592 7.655 19249 Z= 0.357 Chirality : 0.036 0.121 2192 Planarity : 0.005 0.049 1372 Dihedral : 31.448 170.025 4202 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 15.59 % Favored : 83.02 % 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: 2.71 (0.29), residues: 758 helix: 2.54 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.28 (0.36), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG D 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5531.93 seconds wall clock time: 97 minutes 37.27 seconds (5857.27 seconds total)