Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:01:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/11_2022/7p14_13155_updated.pdb" } resolution = 3.66 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= 0.002 sd= 0.046 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 138": "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: 3796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2706 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PLC': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 2.75, per 1000 atoms: 0.72 Number of scatterers: 3796 At special positions: 0 Unit cell: (96.348, 69.006, 70.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 3 15.00 O 656 8.00 N 579 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " distance=2.03 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: 1.60 Conformation dependent library (CDL) restraints added in 683.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 61.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.515A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 66 removed outlier: 3.741A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 88 through 104 removed outlier: 3.530A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 157 removed outlier: 3.590A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 3.572A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.504A pdb=" N ARG A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 5.032A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 removed outlier: 3.654A pdb=" N LEU A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 249 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.733A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 307 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.616A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.725A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 678 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: 1.05 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 545 1.32 - 1.44: 1168 1.44 - 1.56: 2136 1.56 - 1.69: 6 1.69 - 1.81: 37 Bond restraints: 3892 Sorted by residual: bond pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" C3 P5S A 403 " pdb=" O16 P5S A 403 " ideal model delta sigma weight residual 1.405 1.456 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C4 PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C4 PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 PLC A 402 " pdb=" O3P PLC A 402 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3887 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.77: 39 104.77 - 112.09: 1914 112.09 - 119.40: 1221 119.40 - 126.72: 2040 126.72 - 134.04: 56 Bond angle restraints: 5270 Sorted by residual: angle pdb=" O3P PLC A 402 " pdb=" P PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 93.62 104.20 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 103.08 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C3 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 107.38 114.66 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" CA LYS A 284 " pdb=" CB LYS A 284 " pdb=" CG LYS A 284 " ideal model delta sigma weight residual 114.10 118.68 -4.58 2.00e+00 2.50e-01 5.24e+00 angle pdb=" CA LEU A 330 " pdb=" CB LEU A 330 " pdb=" CG LEU A 330 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.65e+00 ... (remaining 5265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 2014 22.82 - 45.64: 172 45.64 - 68.45: 19 68.45 - 91.27: 9 91.27 - 114.09: 2 Dihedral angle restraints: 2216 sinusoidal: 887 harmonic: 1329 Sorted by residual: dihedral pdb=" C27 P5S A 403 " pdb=" C28 P5S A 403 " pdb=" C29 P5S A 403 " pdb=" C30 P5S A 403 " ideal model delta sinusoidal sigma weight residual -179.38 -65.29 -114.09 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA ILE A 319 " pdb=" C ILE A 319 " pdb=" N PRO A 320 " pdb=" CA PRO A 320 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" C41 P5S A 403 " pdb=" C42 P5S A 403 " pdb=" C43 P5S A 403 " pdb=" C44 P5S A 403 " ideal model delta sinusoidal sigma weight residual 181.47 89.64 91.83 1 3.00e+01 1.11e-03 1.10e+01 ... (remaining 2213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 508 0.053 - 0.106: 74 0.106 - 0.159: 4 0.159 - 0.213: 0 0.213 - 0.266: 1 Chirality restraints: 587 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.05 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" C PRO A 201 " pdb=" CB PRO A 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 584 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 319 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 320 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 200 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 201 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 33 " -0.005 2.00e-02 2.50e+03 9.48e-03 8.99e-01 pdb=" C ASN B 33 " 0.016 2.00e-02 2.50e+03 pdb=" O ASN B 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE B 34 " -0.005 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1091 2.82 - 3.34: 3686 3.34 - 3.86: 5967 3.86 - 4.38: 7145 4.38 - 4.90: 12071 Nonbonded interactions: 29960 Sorted by model distance: nonbonded pdb=" OE1 GLU A 260 " pdb=" NH2 ARG A 264 " model vdw 2.295 2.520 nonbonded pdb=" O ILE A 16 " pdb=" OG1 THR A 20 " model vdw 2.369 2.440 nonbonded pdb=" OH TYR A 182 " pdb=" O LEU A 371 " model vdw 2.372 2.440 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.393 2.440 nonbonded pdb=" OH TYR A 208 " pdb=" OH TYR A 291 " model vdw 2.419 2.440 ... (remaining 29955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 25 5.16 5 C 2533 2.51 5 N 579 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 1.610 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.440 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.004 0.051 3892 Z= 0.305 Angle : 0.638 10.583 5270 Z= 0.289 Chirality : 0.037 0.266 587 Planarity : 0.004 0.064 624 Dihedral : 16.560 114.091 1367 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.40), residues: 444 helix: 1.37 (0.31), residues: 257 sheet: 1.11 (0.70), residues: 52 loop : -0.55 (0.57), residues: 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.472 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1358 time to fit residues: 12.5657 Evaluate side-chains 62 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3892 Z= 0.182 Angle : 0.556 6.651 5270 Z= 0.279 Chirality : 0.038 0.126 587 Planarity : 0.004 0.039 624 Dihedral : 12.075 73.650 572 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.02 % 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: 2.14 (0.39), residues: 444 helix: 2.49 (0.30), residues: 258 sheet: 0.98 (0.69), residues: 52 loop : -0.56 (0.57), residues: 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.415 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1312 time to fit residues: 12.8371 Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0374 time to fit residues: 0.8442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 40 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3892 Z= 0.166 Angle : 0.506 5.410 5270 Z= 0.254 Chirality : 0.038 0.178 587 Planarity : 0.003 0.031 624 Dihedral : 10.292 72.869 572 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.76 % 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: 2.51 (0.39), residues: 444 helix: 2.86 (0.29), residues: 262 sheet: 0.97 (0.70), residues: 52 loop : -0.63 (0.57), residues: 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.417 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 67 average time/residue: 0.1344 time to fit residues: 11.6997 Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0380 time to fit residues: 0.8343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3892 Z= 0.181 Angle : 0.504 5.741 5270 Z= 0.253 Chirality : 0.037 0.173 587 Planarity : 0.003 0.027 624 Dihedral : 9.492 71.955 572 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.02 % 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: 2.73 (0.40), residues: 444 helix: 3.09 (0.29), residues: 261 sheet: 1.08 (0.69), residues: 52 loop : -0.67 (0.57), residues: 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.390 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1263 time to fit residues: 11.0633 Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0367 time to fit residues: 0.7836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3892 Z= 0.201 Angle : 0.502 5.812 5270 Z= 0.252 Chirality : 0.038 0.178 587 Planarity : 0.003 0.025 624 Dihedral : 9.013 72.039 572 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 2.83 (0.40), residues: 444 helix: 3.25 (0.29), residues: 259 sheet: 1.12 (0.69), residues: 52 loop : -0.75 (0.56), residues: 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.381 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.1251 time to fit residues: 11.2012 Evaluate side-chains 62 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0534 time to fit residues: 1.0198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3892 Z= 0.221 Angle : 0.524 6.531 5270 Z= 0.262 Chirality : 0.038 0.186 587 Planarity : 0.003 0.023 624 Dihedral : 8.833 72.427 572 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.76 % 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: 2.78 (0.40), residues: 444 helix: 3.21 (0.29), residues: 259 sheet: 1.09 (0.68), residues: 52 loop : -0.74 (0.56), residues: 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.419 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.1374 time to fit residues: 12.4619 Evaluate side-chains 65 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0391 time to fit residues: 0.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3892 Z= 0.199 Angle : 0.523 6.187 5270 Z= 0.260 Chirality : 0.038 0.184 587 Planarity : 0.003 0.045 624 Dihedral : 8.630 72.667 572 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.39), residues: 444 helix: 3.19 (0.29), residues: 259 sheet: 1.05 (0.67), residues: 52 loop : -0.77 (0.56), residues: 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.410 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.1367 time to fit residues: 11.8454 Evaluate side-chains 65 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0466 time to fit residues: 0.9556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3892 Z= 0.270 Angle : 0.560 6.306 5270 Z= 0.282 Chirality : 0.039 0.194 587 Planarity : 0.003 0.030 624 Dihedral : 8.826 74.158 572 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.01 % 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: 2.57 (0.40), residues: 444 helix: 3.01 (0.30), residues: 259 sheet: 1.02 (0.67), residues: 52 loop : -0.77 (0.56), residues: 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.408 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1326 time to fit residues: 11.9574 Evaluate side-chains 65 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0420 time to fit residues: 0.8172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3892 Z= 0.212 Angle : 0.554 6.334 5270 Z= 0.278 Chirality : 0.038 0.191 587 Planarity : 0.003 0.029 624 Dihedral : 8.592 74.229 572 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.76 % 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: 2.59 (0.40), residues: 444 helix: 3.10 (0.29), residues: 258 sheet: 0.93 (0.68), residues: 52 loop : -0.87 (0.55), residues: 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.430 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 59 average time/residue: 0.1081 time to fit residues: 8.8168 Evaluate side-chains 56 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3892 Z= 0.208 Angle : 0.555 6.347 5270 Z= 0.283 Chirality : 0.038 0.193 587 Planarity : 0.003 0.028 624 Dihedral : 8.426 74.224 572 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.50 % 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: 2.49 (0.40), residues: 444 helix: 3.06 (0.30), residues: 256 sheet: 0.88 (0.67), residues: 52 loop : -0.91 (0.54), residues: 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.403 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.1130 time to fit residues: 9.2207 Evaluate side-chains 58 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0379 time to fit residues: 0.6855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 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 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.170437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140219 restraints weight = 4418.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142978 restraints weight = 2958.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145270 restraints weight = 2306.998| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3892 Z= 0.222 Angle : 0.565 7.109 5270 Z= 0.284 Chirality : 0.038 0.196 587 Planarity : 0.003 0.033 624 Dihedral : 8.415 74.498 572 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.76 % 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: 2.50 (0.40), residues: 444 helix: 3.05 (0.30), residues: 256 sheet: 0.84 (0.66), residues: 52 loop : -0.87 (0.54), residues: 136 =============================================================================== Job complete usr+sys time: 1040.01 seconds wall clock time: 19 minutes 39.73 seconds (1179.73 seconds total)