Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 12:17:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoz_33991/04_2023/7yoz_33991.pdb" } resolution = 4.3 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 5365 2.51 5 N 1838 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 83": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "D ARG 36": "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 ARG 134": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ARG 92": "NH1" <-> "NH2" 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: 9752 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: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} 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: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} 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: 5.49, per 1000 atoms: 0.56 Number of scatterers: 9752 At special positions: 0 Unit cell: (122.85, 90.3, 113.4, 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 1838 7.00 C 5365 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: 5.20 Conformation dependent library (CDL) restraints added in 774.4 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 79.1% alpha, 0.7% beta 120 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.614A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.575A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.537A 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 93 removed outlier: 3.512A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.526A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.706A 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 131 removed outlier: 3.563A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.537A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.653A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.818A 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 removed outlier: 3.593A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) 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 'C' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.722A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 350 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.45: 3358 1.45 - 1.57: 4570 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10403 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB ARG G 128 " pdb=" CG ARG G 128 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.40e-02 5.10e+03 1.37e+00 bond pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CE LYS G 64 " pdb=" NZ LYS G 64 " ideal model delta sigma weight residual 1.489 1.457 0.032 3.00e-02 1.11e+03 1.15e+00 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 99.23 - 105.87: 1262 105.87 - 112.52: 5646 112.52 - 119.16: 2709 119.16 - 125.81: 4655 125.81 - 132.45: 796 Bond angle restraints: 15068 Sorted by residual: angle pdb=" CB LEU A 103 " pdb=" CG LEU A 103 " pdb=" CD1 LEU A 103 " ideal model delta sigma weight residual 110.70 103.05 7.65 3.00e+00 1.11e-01 6.50e+00 angle pdb=" N SER C 86 " pdb=" CA SER C 86 " pdb=" C SER C 86 " ideal model delta sigma weight residual 111.07 113.75 -2.68 1.07e+00 8.73e-01 6.25e+00 angle pdb=" CA LEU B 62 " pdb=" CB LEU B 62 " pdb=" CG LEU B 62 " ideal model delta sigma weight residual 116.30 124.22 -7.92 3.50e+00 8.16e-02 5.12e+00 angle pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " pdb=" NH1 ARG B 92 " ideal model delta sigma weight residual 121.50 119.26 2.24 1.00e+00 1.00e+00 5.00e+00 angle pdb=" C LEU B 90 " pdb=" N LYS B 91 " pdb=" CA LYS B 91 " ideal model delta sigma weight residual 120.28 123.27 -2.99 1.34e+00 5.57e-01 4.97e+00 ... (remaining 15063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4337 35.80 - 71.59: 1089 71.59 - 107.39: 15 107.39 - 143.19: 1 143.19 - 178.98: 3 Dihedral angle restraints: 5445 sinusoidal: 3719 harmonic: 1726 Sorted by residual: 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 -140.00 38.98 -178.98 1 3.50e+01 8.16e-04 1.57e+01 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 36.13 -176.13 1 3.50e+01 8.16e-04 1.57e+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 76.24 143.76 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 5442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1559 0.050 - 0.101: 141 0.101 - 0.151: 20 0.151 - 0.201: 1 0.201 - 0.252: 2 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CG LEU A 103 " pdb=" CB LEU A 103 " pdb=" CD1 LEU A 103 " pdb=" CD2 LEU A 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU G 103 " pdb=" CB LEU G 103 " pdb=" CD1 LEU G 103 " pdb=" CD2 LEU G 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA THR G 107 " pdb=" N THR G 107 " pdb=" C THR G 107 " pdb=" CB THR G 107 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1720 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 77 " 0.024 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" CG ASP E 77 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASP E 77 " 0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP E 77 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 31 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO D 32 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.031 9.50e-02 1.11e+02 1.84e-02 1.96e+00 pdb=" NE ARG B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " -0.007 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1872 2.80 - 3.32: 8558 3.32 - 3.85: 18168 3.85 - 4.37: 20847 4.37 - 4.90: 29311 Nonbonded interactions: 78756 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.269 2.520 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.270 2.520 nonbonded pdb=" NZ LYS C 115 " pdb=" OP2 DT J 29 " model vdw 2.324 2.520 nonbonded pdb=" NE ARG G 128 " pdb=" OE1 GLU G 133 " model vdw 2.359 2.520 nonbonded pdb=" NZ LYS G 79 " pdb=" OE1 GLU H 74 " model vdw 2.366 2.520 ... (remaining 78751 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.230 Find NCS groups from input model: 0.400 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.037 10403 Z= 0.171 Angle : 0.552 7.918 15068 Z= 0.361 Chirality : 0.032 0.252 1723 Planarity : 0.004 0.050 1069 Dihedral : 27.621 178.984 4321 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 0.64 (0.30), residues: 578 helix: 0.94 (0.21), residues: 450 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3521 time to fit residues: 143.9212 Evaluate side-chains 213 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8313 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 GLN ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10403 Z= 0.268 Angle : 0.664 6.550 15068 Z= 0.385 Chirality : 0.037 0.133 1723 Planarity : 0.005 0.053 1069 Dihedral : 32.172 179.806 3094 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 0.40 % 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: 1.62 (0.33), residues: 578 helix: 1.65 (0.23), residues: 468 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.3413 time to fit residues: 112.9366 Evaluate side-chains 196 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0882 time to fit residues: 1.1536 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 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: 7.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 10403 Z= 0.265 Angle : 0.643 6.679 15068 Z= 0.379 Chirality : 0.035 0.140 1723 Planarity : 0.005 0.047 1069 Dihedral : 32.237 179.657 3094 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.40 % 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: 1.43 (0.33), residues: 578 helix: 1.44 (0.23), residues: 467 sheet: None (None), residues: 0 loop : -1.03 (0.49), residues: 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 268 average time/residue: 0.3083 time to fit residues: 104.2841 Evaluate side-chains 211 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0836 time to fit residues: 0.9598 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10403 Z= 0.249 Angle : 0.643 5.738 15068 Z= 0.379 Chirality : 0.035 0.165 1723 Planarity : 0.005 0.066 1069 Dihedral : 32.488 179.729 3094 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 1.45 (0.34), residues: 578 helix: 1.44 (0.24), residues: 469 sheet: None (None), residues: 0 loop : -0.98 (0.52), residues: 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2925 time to fit residues: 97.6528 Evaluate side-chains 212 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8586 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8175 moved from start: 0.9393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 10403 Z= 0.282 Angle : 0.668 7.455 15068 Z= 0.394 Chirality : 0.036 0.160 1723 Planarity : 0.005 0.053 1069 Dihedral : 32.885 179.890 3094 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.09 (0.33), residues: 578 helix: 1.19 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -0.99 (0.48), residues: 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.3188 time to fit residues: 108.7209 Evaluate side-chains 216 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8988 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 1.0258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 10403 Z= 0.286 Angle : 0.688 9.644 15068 Z= 0.405 Chirality : 0.036 0.160 1723 Planarity : 0.005 0.046 1069 Dihedral : 33.118 179.573 3094 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 0.72 (0.32), residues: 578 helix: 0.98 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2823 time to fit residues: 96.8011 Evaluate side-chains 222 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8108 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 1.9990 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: 0.9980 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN ** G 93 GLN ** 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: 0.8173 moved from start: 1.0363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10403 Z= 0.214 Angle : 0.668 13.869 15068 Z= 0.383 Chirality : 0.035 0.194 1723 Planarity : 0.004 0.032 1069 Dihedral : 32.801 179.396 3094 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 0.86 (0.33), residues: 578 helix: 1.02 (0.23), residues: 466 sheet: None (None), residues: 0 loop : -1.09 (0.51), residues: 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2921 time to fit residues: 101.1304 Evaluate side-chains 226 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9410 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 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: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN G 93 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: 0.8221 moved from start: 1.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10403 Z= 0.254 Angle : 0.696 13.356 15068 Z= 0.398 Chirality : 0.036 0.171 1723 Planarity : 0.004 0.038 1069 Dihedral : 32.907 179.849 3094 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 0.65 (0.33), residues: 578 helix: 0.92 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2649 time to fit residues: 90.0934 Evaluate side-chains 219 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8357 ------------------------------------------------------------------------------- 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: 10.0000 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 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: 5.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 4.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 93 GLN ** 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: 0.8356 moved from start: 1.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 10403 Z= 0.341 Angle : 0.758 10.967 15068 Z= 0.439 Chirality : 0.040 0.186 1723 Planarity : 0.005 0.048 1069 Dihedral : 33.666 179.848 3094 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.22 (0.33), residues: 578 helix: 0.68 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -1.81 (0.45), residues: 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2870 time to fit residues: 96.1822 Evaluate side-chains 217 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8848 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 1.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 10403 Z= 0.314 Angle : 0.743 9.439 15068 Z= 0.428 Chirality : 0.039 0.205 1723 Planarity : 0.005 0.033 1069 Dihedral : 33.675 179.602 3094 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.13 (0.33), residues: 578 helix: 0.64 (0.23), residues: 467 sheet: None (None), residues: 0 loop : -2.01 (0.44), residues: 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2744 time to fit residues: 94.1933 Evaluate side-chains 223 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8275 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048187 restraints weight = 57623.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049514 restraints weight = 33876.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050390 restraints weight = 23341.842| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 1.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10403 Z= 0.225 Angle : 0.715 12.335 15068 Z= 0.404 Chirality : 0.037 0.151 1723 Planarity : 0.005 0.049 1069 Dihedral : 33.352 179.449 3094 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 0.22 (0.33), residues: 578 helix: 0.70 (0.24), residues: 470 sheet: None (None), residues: 0 loop : -2.08 (0.44), residues: 108 =============================================================================== Job complete usr+sys time: 2089.71 seconds wall clock time: 38 minutes 35.65 seconds (2315.65 seconds total)