Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 12:17:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x57_33010/04_2023/7x57_33010.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 242 5.49 5 S 20 5.16 5 C 5373 2.51 5 N 1845 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9767 At special positions: 0 Unit cell: (120.75, 93.45, 111.3, 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 20 16.00 P 242 15.00 O 2287 8.00 N 1845 7.00 C 5373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 753.2 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 78.8% alpha, 2.0% beta 120 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.798A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 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 63 through 79 removed outlier: 3.517A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.559A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.720A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (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 94 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A 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 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.812A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 118 through 119 358 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 312 hydrogen bonds 624 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1875 1.33 - 1.45: 3371 1.45 - 1.57: 4658 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10418 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG LYS H 77 " pdb=" CD LYS H 77 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB MET B 84 " pdb=" CG MET B 84 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 10413 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.13: 1006 105.13 - 111.98: 5732 111.98 - 118.83: 2674 118.83 - 125.68: 4880 125.68 - 132.53: 794 Bond angle restraints: 15086 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 104.00 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" CA ARG H 92 " pdb=" CB ARG H 92 " pdb=" CG ARG H 92 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 angle pdb=" C ALA F 76 " pdb=" N LYS F 77 " pdb=" CA LYS F 77 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.35e+00 angle pdb=" C TYR D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta sigma weight residual 120.28 116.66 3.62 1.34e+00 5.57e-01 7.31e+00 angle pdb=" N GLY D 56 " pdb=" CA GLY D 56 " pdb=" C GLY D 56 " ideal model delta sigma weight residual 112.50 109.51 2.99 1.16e+00 7.43e-01 6.62e+00 ... (remaining 15081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 4265 34.68 - 69.35: 1156 69.35 - 104.02: 32 104.02 - 138.70: 1 138.70 - 173.37: 3 Dihedral angle restraints: 5457 sinusoidal: 3728 harmonic: 1729 Sorted by residual: dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual 220.00 46.63 173.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 49.06 170.94 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual 220.00 50.32 169.68 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 300 0.072 - 0.108: 78 0.108 - 0.143: 14 0.143 - 0.179: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CB VAL H 70 " pdb=" CA VAL H 70 " pdb=" CG1 VAL H 70 " pdb=" CG2 VAL H 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA LYS H 77 " pdb=" N LYS H 77 " pdb=" C LYS H 77 " pdb=" CB LYS H 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CB ILE F 50 " pdb=" CA ILE F 50 " pdb=" CG1 ILE F 50 " pdb=" CG2 ILE F 50 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1720 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 67 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG B 67 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG B 67 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP B 68 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 49 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C LEU D 49 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU D 49 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 50 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 67 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ARG D 67 " -0.066 2.00e-02 2.50e+03 pdb=" O ARG D 67 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.022 2.00e-02 2.50e+03 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2199 2.81 - 3.33: 9187 3.33 - 3.85: 19761 3.85 - 4.38: 21986 4.38 - 4.90: 30534 Nonbonded interactions: 83667 Sorted by model distance: nonbonded pdb=" NE2 GLN A 125 " pdb=" OE2 GLU B 53 " model vdw 2.286 2.520 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DC I 39 " model vdw 2.322 2.520 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.337 2.520 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.369 2.520 nonbonded pdb=" N SER A 86 " pdb=" OP1 DT J 7 " model vdw 2.375 2.520 ... (remaining 83662 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 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.120 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.210 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.045 10418 Z= 0.196 Angle : 0.633 8.819 15086 Z= 0.411 Chirality : 0.034 0.179 1723 Planarity : 0.007 0.061 1072 Dihedral : 28.984 173.373 4331 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.20 % 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: 0.39 (0.29), residues: 579 helix: 0.79 (0.21), residues: 459 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.3881 time to fit residues: 82.8585 Evaluate side-chains 115 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 93 GLN E 125 GLN G 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.260 Angle : 0.612 6.432 15086 Z= 0.355 Chirality : 0.034 0.129 1723 Planarity : 0.004 0.038 1072 Dihedral : 32.777 172.007 3097 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 4.36 % 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: 2.06 (0.33), residues: 579 helix: 2.06 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.770 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.3057 time to fit residues: 57.5291 Evaluate side-chains 134 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0865 time to fit residues: 3.5173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 10418 Z= 0.361 Angle : 0.659 6.726 15086 Z= 0.380 Chirality : 0.036 0.163 1723 Planarity : 0.005 0.036 1072 Dihedral : 33.369 175.841 3097 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 3.37 % 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: 1.91 (0.34), residues: 579 helix: 2.00 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.784 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 0.2898 time to fit residues: 53.5125 Evaluate side-chains 118 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0890 time to fit residues: 2.3780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 68 GLN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.203 Angle : 0.580 7.950 15086 Z= 0.341 Chirality : 0.033 0.175 1723 Planarity : 0.004 0.034 1072 Dihedral : 33.069 177.410 3097 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.17 % 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: 2.46 (0.34), residues: 579 helix: 2.40 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.729 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2854 time to fit residues: 50.4302 Evaluate side-chains 120 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0850 time to fit residues: 2.3996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10418 Z= 0.233 Angle : 0.596 7.530 15086 Z= 0.347 Chirality : 0.033 0.160 1723 Planarity : 0.004 0.040 1072 Dihedral : 33.060 177.823 3097 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.39 % 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 (0.34), residues: 579 helix: 2.50 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.814 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.2905 time to fit residues: 45.9348 Evaluate side-chains 112 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0966 time to fit residues: 1.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.203 Angle : 0.591 9.313 15086 Z= 0.342 Chirality : 0.033 0.143 1723 Planarity : 0.004 0.038 1072 Dihedral : 32.920 178.350 3097 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.34), residues: 579 helix: 2.61 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.44 (0.44), residues: 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 126 average time/residue: 0.2924 time to fit residues: 47.6074 Evaluate side-chains 115 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0896 time to fit residues: 1.8908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10418 Z= 0.239 Angle : 0.606 8.565 15086 Z= 0.349 Chirality : 0.033 0.144 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.991 179.109 3097 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.39 % 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 (0.34), residues: 579 helix: 2.61 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.783 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2874 time to fit residues: 44.5829 Evaluate side-chains 107 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0984 time to fit residues: 1.6274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.207 Angle : 0.594 9.301 15086 Z= 0.345 Chirality : 0.033 0.143 1723 Planarity : 0.004 0.035 1072 Dihedral : 32.871 179.852 3097 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.58 % 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: 2.85 (0.34), residues: 579 helix: 2.70 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.50 (0.45), residues: 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.782 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.2935 time to fit residues: 43.0778 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0930 time to fit residues: 1.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 25 ASN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10418 Z= 0.230 Angle : 0.619 10.081 15086 Z= 0.353 Chirality : 0.033 0.138 1723 Planarity : 0.004 0.033 1072 Dihedral : 32.897 179.686 3097 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.99 % 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: 2.77 (0.34), residues: 579 helix: 2.66 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.773 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.3001 time to fit residues: 41.9956 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5408 time to fit residues: 1.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 25 ASN E 125 GLN F 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 10418 Z= 0.204 Angle : 0.615 10.482 15086 Z= 0.351 Chirality : 0.033 0.148 1723 Planarity : 0.004 0.035 1072 Dihedral : 32.729 179.680 3097 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.59 % 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: 2.82 (0.34), residues: 579 helix: 2.70 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.703 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.2954 time to fit residues: 41.7296 Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0905 time to fit residues: 1.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 10.0000 chunk 9 optimal weight: 0.0050 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.127236 restraints weight = 19582.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.130000 restraints weight = 12764.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.129872 restraints weight = 10817.714| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10418 Z= 0.196 Angle : 0.617 10.512 15086 Z= 0.351 Chirality : 0.033 0.182 1723 Planarity : 0.004 0.034 1072 Dihedral : 32.634 178.746 3097 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.99 % 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: 2.84 (0.35), residues: 579 helix: 2.71 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -1.65 (0.45), residues: 120 =============================================================================== Job complete usr+sys time: 1626.13 seconds wall clock time: 30 minutes 23.97 seconds (1823.97 seconds total)