Starting phenix.real_space_refine (version: dev) on Sun Feb 19 08:33:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x58_33011/02_2023/7x58_33011.pdb" } resolution = 3.93 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 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 23": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9775 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} 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: 5.91, per 1000 atoms: 0.60 Number of scatterers: 9775 At special positions: 0 Unit cell: (121.8, 95.55, 110.25, 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 2290 8.00 N 1846 7.00 C 5377 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: 5.38 Conformation dependent library (CDL) restraints added in 752.7 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 79.9% alpha, 2.3% beta 117 base pairs and 201 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.748A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.585A 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 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) 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 95 removed outlier: 3.674A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 78 " --> pdb=" O ILE C 74 " (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: 3.542A 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 removed outlier: 3.529A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.511A 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 131 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.848A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 25 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 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.793A 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 removed outlier: 3.637A pdb=" N ILE C 119 " --> pdb=" O ARG D 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.198A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.666A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 119 357 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 303 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 201 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 5.68 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: 1842 1.33 - 1.45: 3403 1.45 - 1.57: 4667 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10426 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CG LEU B 62 " pdb=" CD2 LEU B 62 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" C MET C 120 " pdb=" N PRO C 121 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.51e-02 4.39e+03 9.46e-01 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 99.35 - 105.97: 1336 105.97 - 112.58: 5606 112.58 - 119.20: 2725 119.20 - 125.81: 4635 125.81 - 132.43: 795 Bond angle restraints: 15097 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 112.43 109.34 3.09 9.20e-01 1.18e+00 1.13e+01 angle pdb=" CA ARG A 131 " pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " ideal model delta sigma weight residual 111.30 104.47 6.83 2.30e+00 1.89e-01 8.82e+00 angle pdb=" C ALA C 114 " pdb=" N LYS C 115 " pdb=" CA LYS C 115 " ideal model delta sigma weight residual 122.61 126.28 -3.67 1.56e+00 4.11e-01 5.54e+00 angle pdb=" C ARG D 78 " pdb=" N LYS D 79 " pdb=" CA LYS D 79 " ideal model delta sigma weight residual 121.54 125.74 -4.20 1.91e+00 2.74e-01 4.85e+00 ... (remaining 15092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 4380 35.47 - 70.94: 1067 70.94 - 106.41: 11 106.41 - 141.88: 1 141.88 - 177.36: 3 Dihedral angle restraints: 5462 sinusoidal: 3730 harmonic: 1732 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 -140.00 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+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 53.77 166.23 1 3.50e+01 8.16e-04 1.54e+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 74.13 145.87 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 5459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1612 0.062 - 0.124: 104 0.124 - 0.185: 6 0.185 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CG LEU H 62 " pdb=" CB LEU H 62 " pdb=" CD1 LEU H 62 " pdb=" CD2 LEU H 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG A 131 " pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CB ARG A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1721 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 32 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 31 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO H 32 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 66 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.015 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1171 2.76 - 3.29: 8687 3.29 - 3.83: 19177 3.83 - 4.36: 22265 4.36 - 4.90: 30841 Nonbonded interactions: 82141 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.221 2.440 nonbonded pdb=" NH2 ARG G 63 " pdb=" OP1 DA I 18 " model vdw 2.267 2.520 nonbonded pdb=" O2 DT I -24 " pdb=" N2 DG J 25 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.293 2.520 nonbonded pdb=" NH2 ARG C 72 " pdb=" OP1 DC I -54 " model vdw 2.345 2.520 ... (remaining 82136 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 24 through 95) selection = chain 'D' selection = chain 'F' selection = (chain 'H' and resid 24 through 95) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 5377 2.51 5 N 1846 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.250 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: 2.170 Check model and map are aligned: 0.150 Process input model: 32.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 0.041 10426 Z= 0.176 Angle : 0.565 6.829 15097 Z= 0.367 Chirality : 0.032 0.309 1724 Planarity : 0.003 0.033 1074 Dihedral : 27.305 177.356 4334 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 580 helix: 1.04 (0.21), residues: 434 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3526 time to fit residues: 125.2034 Evaluate side-chains 162 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8785 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 64 ASN F 75 HIS G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 10426 Z= 0.276 Angle : 0.638 9.075 15097 Z= 0.371 Chirality : 0.035 0.151 1724 Planarity : 0.004 0.055 1074 Dihedral : 31.954 175.490 3098 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 4.74 % 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: 2.74 (0.33), residues: 580 helix: 2.67 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 191 average time/residue: 0.2851 time to fit residues: 70.7924 Evaluate side-chains 159 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1127 time to fit residues: 3.6611 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 10426 Z= 0.396 Angle : 0.696 8.028 15097 Z= 0.403 Chirality : 0.038 0.187 1724 Planarity : 0.004 0.027 1074 Dihedral : 32.754 175.534 3098 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 6.92 % 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 (0.33), residues: 580 helix: 2.49 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.67 (0.41), residues: 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 187 average time/residue: 0.2698 time to fit residues: 65.9035 Evaluate side-chains 171 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1238 time to fit residues: 4.4158 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.242 Angle : 0.633 7.191 15097 Z= 0.370 Chirality : 0.035 0.157 1724 Planarity : 0.004 0.025 1074 Dihedral : 32.578 175.741 3098 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.33), residues: 580 helix: 2.62 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.74 (0.42), residues: 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 199 average time/residue: 0.2607 time to fit residues: 68.3234 Evaluate side-chains 169 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0889 time to fit residues: 3.2080 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.225 Angle : 0.634 8.352 15097 Z= 0.367 Chirality : 0.035 0.160 1724 Planarity : 0.004 0.027 1074 Dihedral : 32.462 176.406 3098 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.37 % 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: 2.62 (0.34), residues: 580 helix: 2.64 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 0.797 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 176 average time/residue: 0.2620 time to fit residues: 60.9619 Evaluate side-chains 161 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0860 time to fit residues: 2.1176 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10426 Z= 0.256 Angle : 0.651 8.276 15097 Z= 0.375 Chirality : 0.036 0.213 1724 Planarity : 0.004 0.042 1074 Dihedral : 32.557 176.117 3098 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.77 % 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: 2.47 (0.33), residues: 580 helix: 2.54 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 0.752 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 171 average time/residue: 0.2622 time to fit residues: 59.0995 Evaluate side-chains 168 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1179 time to fit residues: 2.8070 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10426 Z= 0.217 Angle : 0.656 9.220 15097 Z= 0.373 Chirality : 0.035 0.193 1724 Planarity : 0.004 0.032 1074 Dihedral : 32.442 176.544 3098 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.57 % 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: 2.42 (0.33), residues: 580 helix: 2.49 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 0.702 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 179 average time/residue: 0.2680 time to fit residues: 63.0690 Evaluate side-chains 169 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1588 time to fit residues: 2.5204 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 10426 Z= 0.354 Angle : 0.717 9.244 15097 Z= 0.407 Chirality : 0.038 0.204 1724 Planarity : 0.004 0.049 1074 Dihedral : 32.980 175.598 3098 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.33), residues: 580 helix: 2.31 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.88 (0.40), residues: 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 0.767 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 164 average time/residue: 0.2567 time to fit residues: 56.2115 Evaluate side-chains 155 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1303 time to fit residues: 2.1500 ------------------------------------------------------------------------------- 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: 8.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 10426 Z= 0.302 Angle : 0.703 10.198 15097 Z= 0.398 Chirality : 0.037 0.218 1724 Planarity : 0.004 0.041 1074 Dihedral : 32.920 175.436 3098 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.78 % 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: 2.19 (0.33), residues: 580 helix: 2.29 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.78 (0.40), residues: 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 0.746 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 166 average time/residue: 0.2500 time to fit residues: 55.0474 Evaluate side-chains 158 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0824 time to fit residues: 1.2825 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 10426 Z= 0.296 Angle : 0.712 10.768 15097 Z= 0.399 Chirality : 0.037 0.194 1724 Planarity : 0.004 0.038 1074 Dihedral : 32.919 175.722 3098 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.19 % 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: 2.15 (0.33), residues: 580 helix: 2.26 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.728 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 162 average time/residue: 0.2530 time to fit residues: 54.8155 Evaluate side-chains 158 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0870 time to fit residues: 1.2182 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061479 restraints weight = 31864.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063082 restraints weight = 18906.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064141 restraints weight = 13918.260| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10426 Z= 0.236 Angle : 0.694 11.041 15097 Z= 0.389 Chirality : 0.035 0.187 1724 Planarity : 0.004 0.039 1074 Dihedral : 32.682 176.142 3098 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.19 % 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: 2.26 (0.33), residues: 580 helix: 2.33 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.64 (0.42), residues: 130 =============================================================================== Job complete usr+sys time: 1688.57 seconds wall clock time: 31 minutes 35.95 seconds (1895.95 seconds total)