Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 07:53:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/04_2023/7sau_24957.pdb" } resolution = 3.0 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= 0.005 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4140 2.51 5 N 1018 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "F TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" 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: 6317 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1749 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1731 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "C" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 3.88, per 1000 atoms: 0.61 Number of scatterers: 6317 At special positions: 0 Unit cell: (70.72, 69.056, 134.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1135 8.00 N 1018 7.00 C 4140 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: 2.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 29 through 68 removed outlier: 3.795A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 104 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 190 through 219 Proline residue: A 196 - end of helix removed outlier: 3.697A pdb=" N ASN A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 4.738A pdb=" N LEU B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 19 " --> pdb=" O MET B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 66 removed outlier: 3.781A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 103 removed outlier: 3.567A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 152 removed outlier: 4.309A pdb=" N GLU B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.537A pdb=" N PHE B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 190 through 218 Proline residue: B 196 - end of helix removed outlier: 3.689A pdb=" N HIS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 39 through 59 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.623A pdb=" N ILE D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'E' and resid 8 through 36 removed outlier: 3.614A pdb=" N LYS E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 14 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.517A pdb=" N PHE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 3.532A pdb=" N MET F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 59 " --> pdb=" O PHE F 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.503A pdb=" N PHE G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.727A pdb=" N VAL A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 2.69 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: 1979 1.34 - 1.46: 920 1.46 - 1.57: 3508 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 6455 Sorted by residual: bond pdb=" CB PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.35e+00 bond pdb=" CG1 ILE B 28 " pdb=" CD1 ILE B 28 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.23e+00 bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 6450 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 119 106.20 - 113.15: 3494 113.15 - 120.09: 2327 120.09 - 127.03: 2719 127.03 - 133.98: 58 Bond angle restraints: 8717 Sorted by residual: angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" N GLU B 121 " ideal model delta sigma weight residual 116.84 122.70 -5.86 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C MET B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 120.31 115.17 5.14 1.52e+00 4.33e-01 1.14e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 110.80 117.77 -6.97 2.13e+00 2.20e-01 1.07e+01 angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" O ARG B 120 " ideal model delta sigma weight residual 120.51 116.47 4.04 1.43e+00 4.89e-01 7.97e+00 angle pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " ideal model delta sigma weight residual 111.30 117.73 -6.43 2.30e+00 1.89e-01 7.82e+00 ... (remaining 8712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3427 17.04 - 34.07: 343 34.07 - 51.11: 48 51.11 - 68.15: 14 68.15 - 85.19: 5 Dihedral angle restraints: 3837 sinusoidal: 1542 harmonic: 2295 Sorted by residual: dihedral pdb=" CA GLU A 131 " pdb=" C GLU A 131 " pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TRP D 37 " pdb=" C TRP D 37 " pdb=" N THR D 38 " pdb=" CA THR D 38 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N THR F 38 " pdb=" CA THR F 38 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 539 0.029 - 0.058: 304 0.058 - 0.086: 89 0.086 - 0.115: 37 0.115 - 0.144: 5 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA ASP A 211 " pdb=" N ASP A 211 " pdb=" C ASP A 211 " pdb=" CB ASP A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA GLN B 151 " pdb=" N GLN B 151 " pdb=" C GLN B 151 " pdb=" CB GLN B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 971 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 73 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO G 74 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 73 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 74 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 73 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO E 74 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.025 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 66 2.68 - 3.23: 6309 3.23 - 3.79: 9837 3.79 - 4.34: 13280 4.34 - 4.90: 21807 Nonbonded interactions: 51299 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OE2 GLU B 209 " model vdw 2.122 2.440 nonbonded pdb=" OD2 ASP A 62 " pdb=" OH TYR A 80 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 58 " pdb=" OE2 GLU A 209 " model vdw 2.238 2.440 nonbonded pdb=" O ASN B 119 " pdb=" ND2 ASN B 119 " model vdw 2.314 2.520 nonbonded pdb=" OD1 ASN B 125 " pdb=" N TYR B 126 " model vdw 2.359 2.520 ... (remaining 51294 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' and resid 5 through 220) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and resid 6 through 76) selection = (chain 'F' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'G' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 4.170 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.880 Find NCS groups from input model: 0.360 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.005 0.077 6455 Z= 0.309 Angle : 0.606 7.370 8717 Z= 0.331 Chirality : 0.040 0.144 974 Planarity : 0.005 0.110 1095 Dihedral : 13.767 85.186 2353 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.15 % 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: 777 helix: 0.82 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.46 (0.48), residues: 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.796 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 1.2802 time to fit residues: 208.5537 Evaluate side-chains 109 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 40 ASN B 91 ASN B 148 ASN D 36 HIS F 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 6455 Z= 0.177 Angle : 0.522 7.450 8717 Z= 0.274 Chirality : 0.037 0.114 974 Planarity : 0.005 0.077 1095 Dihedral : 4.109 19.780 833 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 2.12 % 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: 1.60 (0.31), residues: 777 helix: 1.63 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.59 (0.48), residues: 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.745 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 135 average time/residue: 1.2810 time to fit residues: 180.7444 Evaluate side-chains 110 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.8188 time to fit residues: 2.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6455 Z= 0.166 Angle : 0.505 7.444 8717 Z= 0.262 Chirality : 0.037 0.115 974 Planarity : 0.004 0.064 1095 Dihedral : 3.978 19.396 833 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 2.12 % 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: 1.96 (0.31), residues: 777 helix: 1.96 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.73 (0.48), residues: 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.732 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 120 average time/residue: 1.2081 time to fit residues: 152.1058 Evaluate side-chains 107 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1023 time to fit residues: 1.3293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS B 85 GLN B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 6455 Z= 0.158 Angle : 0.492 7.887 8717 Z= 0.256 Chirality : 0.037 0.119 974 Planarity : 0.004 0.054 1095 Dihedral : 3.905 19.164 833 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.27 % 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: 2.11 (0.31), residues: 777 helix: 2.11 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.78 (0.48), residues: 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.758 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 123 average time/residue: 1.1548 time to fit residues: 149.4454 Evaluate side-chains 110 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0625 time to fit residues: 1.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 66 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 219 ASN B 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 6455 Z= 0.292 Angle : 0.576 7.975 8717 Z= 0.299 Chirality : 0.041 0.193 974 Planarity : 0.004 0.050 1095 Dihedral : 4.173 19.981 833 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 3.48 % 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: 1.78 (0.31), residues: 777 helix: 1.86 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -0.90 (0.48), residues: 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.745 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 122 average time/residue: 1.1368 time to fit residues: 145.8074 Evaluate side-chains 118 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.3021 time to fit residues: 3.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6455 Z= 0.201 Angle : 0.525 8.372 8717 Z= 0.273 Chirality : 0.039 0.158 974 Planarity : 0.004 0.048 1095 Dihedral : 4.059 20.018 833 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.31), residues: 777 helix: 2.04 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.87 (0.47), residues: 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.767 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 122 average time/residue: 1.1701 time to fit residues: 150.0706 Evaluate side-chains 116 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1059 time to fit residues: 1.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 6455 Z= 0.234 Angle : 0.545 8.546 8717 Z= 0.281 Chirality : 0.039 0.158 974 Planarity : 0.004 0.047 1095 Dihedral : 4.073 19.734 833 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.31), residues: 777 helix: 1.98 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -0.96 (0.47), residues: 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 1.1852 time to fit residues: 151.8762 Evaluate side-chains 118 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.3763 time to fit residues: 3.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6455 Z= 0.170 Angle : 0.519 8.970 8717 Z= 0.268 Chirality : 0.038 0.139 974 Planarity : 0.004 0.052 1095 Dihedral : 3.962 19.116 833 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.82 % 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: 2.20 (0.31), residues: 777 helix: 2.26 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -0.89 (0.46), residues: 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.803 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 117 average time/residue: 1.1638 time to fit residues: 143.2124 Evaluate side-chains 111 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1020 time to fit residues: 1.1862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN G 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6455 Z= 0.185 Angle : 0.516 9.116 8717 Z= 0.267 Chirality : 0.038 0.138 974 Planarity : 0.004 0.046 1095 Dihedral : 3.918 19.118 833 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 2.12 % 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: 2.20 (0.31), residues: 777 helix: 2.24 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.86 (0.46), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.793 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 1.1492 time to fit residues: 136.6195 Evaluate side-chains 111 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1030 time to fit residues: 1.3459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6455 Z= 0.211 Angle : 0.533 9.285 8717 Z= 0.277 Chirality : 0.039 0.132 974 Planarity : 0.004 0.045 1095 Dihedral : 3.951 19.367 833 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.97 % 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: 2.16 (0.31), residues: 777 helix: 2.20 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.677 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 1.1637 time to fit residues: 138.1803 Evaluate side-chains 109 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0989 time to fit residues: 1.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103753 restraints weight = 7218.170| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.73 r_work: 0.2941 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6455 Z= 0.158 Angle : 0.513 8.184 8717 Z= 0.265 Chirality : 0.037 0.128 974 Planarity : 0.004 0.058 1095 Dihedral : 3.840 18.904 833 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.21 % 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: 2.38 (0.31), residues: 777 helix: 2.38 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.82 (0.47), residues: 204 =============================================================================== Job complete usr+sys time: 2811.70 seconds wall clock time: 50 minutes 26.14 seconds (3026.14 seconds total)