Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:28:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk1_25169/11_2022/7sk1_25169_updated.pdb" } resolution = 3.43 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= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B GLU 265": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4291 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {' K': 3, 'C14': 1, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'C14': 1, 'OCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.90, per 1000 atoms: 0.68 Number of scatterers: 4291 At special positions: 0 Unit cell: (70.245, 56.865, 98.12, 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) K 3 19.00 S 18 16.00 O 724 8.00 N 666 7.00 C 2880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 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: 2.02 Conformation dependent library (CDL) restraints added in 642.1 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 21 through 67 removed outlier: 3.505A pdb=" N VAL A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 5.110A pdb=" N LYS A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 66 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.921A pdb=" N GLN A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 128 through 160 removed outlier: 3.610A pdb=" N ALA A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.525A pdb=" N HIS A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 242 through 269 removed outlier: 4.030A pdb=" N GLU A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'B' and resid 21 through 67 removed outlier: 3.504A pdb=" N VAL B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 5.111A pdb=" N LYS B 60 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 66 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.920A pdb=" N GLN B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 128 through 160 removed outlier: 3.610A pdb=" N ALA B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.526A pdb=" N HIS B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.566A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 242 through 269 removed outlier: 4.029A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 282 hydrogen bonds defined for protein. 630 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: 1.02 Time building geometry restraints manager: 2.09 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: 1274 1.34 - 1.46: 1093 1.46 - 1.58: 2019 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4408 Sorted by residual: bond pdb=" CB TRP B 100 " pdb=" CG TRP B 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.63e+00 bond pdb=" CB TRP A 100 " pdb=" CG TRP A 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CG LEU B 115 " pdb=" CD1 LEU B 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 ... (remaining 4403 not shown) Histogram of bond angle deviations from ideal: 101.38 - 107.97: 146 107.97 - 114.56: 2393 114.56 - 121.16: 2446 121.16 - 127.75: 937 127.75 - 134.34: 48 Bond angle restraints: 5970 Sorted by residual: angle pdb=" CA LYS B 246 " pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA LYS A 246 " pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " pdb=" CD LYS A 246 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " pdb=" CD LYS B 246 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CG LYS A 274 " pdb=" CD LYS A 274 " pdb=" CE LYS A 274 " ideal model delta sigma weight residual 111.30 118.11 -6.81 2.30e+00 1.89e-01 8.76e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.12: 2293 16.12 - 32.24: 168 32.24 - 48.35: 34 48.35 - 64.46: 2 64.46 - 80.58: 10 Dihedral angle restraints: 2507 sinusoidal: 987 harmonic: 1520 Sorted by residual: dihedral pdb=" CA LEU B 223 " pdb=" C LEU B 223 " pdb=" N SER B 224 " pdb=" CA SER B 224 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 223 " pdb=" C LEU A 223 " pdb=" N SER A 224 " pdb=" CA SER A 224 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN B 99 " pdb=" CB ASN B 99 " pdb=" CG ASN B 99 " pdb=" OD1 ASN B 99 " ideal model delta sinusoidal sigma weight residual 120.00 -173.61 -66.39 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 2504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 428 0.046 - 0.093: 157 0.093 - 0.139: 67 0.139 - 0.185: 14 0.185 - 0.232: 2 Chirality restraints: 668 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 665 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 48 " -0.028 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR A 48 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 48 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 48 " -0.028 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 48 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 48 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 156 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C VAL A 156 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 156 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 1384 2.83 - 3.41: 5313 3.41 - 3.99: 7889 3.99 - 4.56: 11211 4.56 - 5.14: 15919 Nonbonded interactions: 41716 Sorted by model distance: nonbonded pdb=" OD1 ASP A 128 " pdb=" N GLY A 129 " model vdw 2.254 2.520 nonbonded pdb=" OD1 ASP B 128 " pdb=" N GLY B 129 " model vdw 2.254 2.520 nonbonded pdb=" O ASN B 99 " pdb=" ND2 ASN B 99 " model vdw 2.286 2.520 nonbonded pdb=" O ASN A 99 " pdb=" ND2 ASN A 99 " model vdw 2.287 2.520 nonbonded pdb=" OH TYR A 120 " pdb=" OG SER A 222 " model vdw 2.358 2.440 ... (remaining 41711 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 20 through 281) selection = (chain 'B' and resid 20 through 281) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 18 5.16 5 C 2880 2.51 5 N 666 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.400 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: 0.000 Extract box with map and model: 1.950 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.009 0.059 4408 Z= 0.555 Angle : 1.065 9.548 5970 Z= 0.564 Chirality : 0.058 0.232 668 Planarity : 0.006 0.035 728 Dihedral : 12.815 80.576 1532 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.43 % 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 (0.37), residues: 520 helix: 1.51 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -2.07 (0.61), residues: 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.496 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.1739 time to fit residues: 18.0647 Evaluate side-chains 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 4408 Z= 0.208 Angle : 0.616 5.791 5970 Z= 0.341 Chirality : 0.039 0.134 668 Planarity : 0.006 0.031 728 Dihedral : 5.222 56.423 602 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.36), residues: 520 helix: 0.99 (0.24), residues: 412 sheet: None (None), residues: 0 loop : -2.35 (0.61), residues: 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 99 average time/residue: 0.1575 time to fit residues: 19.6854 Evaluate side-chains 84 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0467 time to fit residues: 1.2403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 4408 Z= 0.190 Angle : 0.547 5.739 5970 Z= 0.299 Chirality : 0.039 0.168 668 Planarity : 0.005 0.034 728 Dihedral : 5.166 58.030 602 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.36), residues: 520 helix: 0.92 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.40 (0.57), residues: 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.491 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 95 average time/residue: 0.1476 time to fit residues: 18.1488 Evaluate side-chains 83 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0427 time to fit residues: 0.7631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 4408 Z= 0.307 Angle : 0.612 5.844 5970 Z= 0.329 Chirality : 0.039 0.130 668 Planarity : 0.005 0.032 728 Dihedral : 5.499 57.366 602 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 3.91 % 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: 0.23 (0.37), residues: 520 helix: 0.89 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.60 (0.54), residues: 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.1588 time to fit residues: 19.5874 Evaluate side-chains 96 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0464 time to fit residues: 1.8571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 4408 Z= 0.209 Angle : 0.541 5.697 5970 Z= 0.295 Chirality : 0.037 0.123 668 Planarity : 0.005 0.031 728 Dihedral : 5.320 57.013 602 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 1.96 % 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: 0.30 (0.37), residues: 520 helix: 0.89 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.41 (0.55), residues: 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.509 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 89 average time/residue: 0.1549 time to fit residues: 17.5930 Evaluate side-chains 87 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0505 time to fit residues: 0.9239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4408 Z= 0.219 Angle : 0.568 8.245 5970 Z= 0.307 Chirality : 0.037 0.126 668 Planarity : 0.005 0.029 728 Dihedral : 5.280 57.176 602 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.37), residues: 520 helix: 0.82 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.54 (0.53), residues: 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.498 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 95 average time/residue: 0.1733 time to fit residues: 20.6752 Evaluate side-chains 87 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0469 time to fit residues: 1.2670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.0570 chunk 30 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4408 Z= 0.181 Angle : 0.546 6.568 5970 Z= 0.294 Chirality : 0.037 0.121 668 Planarity : 0.005 0.028 728 Dihedral : 5.144 58.245 602 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.37), residues: 520 helix: 0.83 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -2.45 (0.54), residues: 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.439 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 0.1677 time to fit residues: 19.8488 Evaluate side-chains 89 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0434 time to fit residues: 0.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 4408 Z= 0.176 Angle : 0.533 8.166 5970 Z= 0.287 Chirality : 0.037 0.129 668 Planarity : 0.005 0.029 728 Dihedral : 5.116 58.237 602 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.30 % 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: 0.24 (0.37), residues: 520 helix: 0.88 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.56 (0.53), residues: 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.365 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.1361 time to fit residues: 15.3152 Evaluate side-chains 87 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0440 time to fit residues: 0.9172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 4408 Z= 0.186 Angle : 0.562 9.042 5970 Z= 0.299 Chirality : 0.037 0.130 668 Planarity : 0.006 0.071 728 Dihedral : 5.125 58.183 602 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.65 % 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: 0.17 (0.37), residues: 520 helix: 0.81 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.50 (0.54), residues: 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.427 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 0.1592 time to fit residues: 17.3406 Evaluate side-chains 83 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0424 time to fit residues: 0.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 4408 Z= 0.161 Angle : 0.536 7.409 5970 Z= 0.290 Chirality : 0.036 0.125 668 Planarity : 0.005 0.060 728 Dihedral : 5.048 59.324 602 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.87 % 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: 0.17 (0.37), residues: 520 helix: 0.84 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -2.64 (0.51), residues: 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.498 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 86 average time/residue: 0.1639 time to fit residues: 17.9232 Evaluate side-chains 82 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0458 time to fit residues: 1.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** 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 = 0.3854 r_free = 0.3854 target = 0.150554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126264 restraints weight = 6221.001| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.66 r_work: 0.3569 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.3552 rms_B_bonded: 2.46 restraints_weight: 0.1250 r_work: 0.3543 rms_B_bonded: 2.50 restraints_weight: 0.0625 r_work: 0.3534 rms_B_bonded: 2.57 restraints_weight: 0.0312 r_work: 0.3524 rms_B_bonded: 2.66 restraints_weight: 0.0156 r_work: 0.3515 rms_B_bonded: 2.77 restraints_weight: 0.0078 r_work: 0.3505 rms_B_bonded: 2.89 restraints_weight: 0.0039 r_work: 0.3494 rms_B_bonded: 3.03 restraints_weight: 0.0020 r_work: 0.3483 rms_B_bonded: 3.19 restraints_weight: 0.0010 r_work: 0.3472 rms_B_bonded: 3.36 restraints_weight: 0.0005 r_work: 0.3460 rms_B_bonded: 3.56 restraints_weight: 0.0002 r_work: 0.3448 rms_B_bonded: 3.77 restraints_weight: 0.0001 r_work: 0.3436 rms_B_bonded: 4.00 restraints_weight: 0.0001 r_work: 0.3422 rms_B_bonded: 4.25 restraints_weight: 0.0000 r_work: 0.3408 rms_B_bonded: 4.52 restraints_weight: 0.0000 r_work: 0.3394 rms_B_bonded: 4.82 restraints_weight: 0.0000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4408 Z= 0.179 Angle : 0.534 7.505 5970 Z= 0.291 Chirality : 0.036 0.127 668 Planarity : 0.005 0.057 728 Dihedral : 5.003 58.919 602 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.43 % 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: 0.11 (0.37), residues: 520 helix: 0.80 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.60 (0.53), residues: 110 =============================================================================== Job complete usr+sys time: 1177.65 seconds wall clock time: 22 minutes 22.08 seconds (1342.08 seconds total)