Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:52:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/04_2023/6m49_30074_updated.pdb" } resolution = 3.7 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= 0.007 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2049 2.51 5 N 495 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1382 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1687 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'HC3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.78 Number of scatterers: 3098 At special positions: 0 Unit cell: (85.873, 78.264, 75.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 537 8.00 N 495 7.00 C 2049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 536.6 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 19 through 50 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 73 through 95 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 213 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 27 through 46 Proline residue: B 43 - end of helix removed outlier: 3.765A pdb=" N LYS B 46 " --> pdb=" O TYR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 304 Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 313 through 337 removed outlier: 4.115A pdb=" N GLY B 332 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 335 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 359 through 369 removed outlier: 4.968A pdb=" N LEU B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 389 through 407 Processing helix chain 'B' and resid 412 through 448 removed outlier: 4.347A pdb=" N THR B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 245 hydrogen bonds defined for protein. 675 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: 0.79 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 944 1.34 - 1.46: 744 1.46 - 1.58: 1450 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3163 Sorted by residual: bond pdb=" N VAL B 309 " pdb=" CA VAL B 309 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.09e+00 bond pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.81e+00 bond pdb=" N GLU B 376 " pdb=" CA GLU B 376 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.27e-02 6.20e+03 7.79e+00 bond pdb=" N GLN A 50 " pdb=" CA GLN A 50 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.32e+00 bond pdb=" N VAL B 377 " pdb=" CA VAL B 377 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.97e+00 ... (remaining 3158 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.36: 49 105.36 - 112.54: 1763 112.54 - 119.72: 989 119.72 - 126.91: 1483 126.91 - 134.09: 41 Bond angle restraints: 4325 Sorted by residual: angle pdb=" CA VAL B 309 " pdb=" C VAL B 309 " pdb=" O VAL B 309 " ideal model delta sigma weight residual 121.58 117.64 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ASP B 374 " pdb=" C ASP B 374 " pdb=" O ASP B 374 " ideal model delta sigma weight residual 120.66 116.41 4.25 1.15e+00 7.56e-01 1.36e+01 angle pdb=" C ASP B 307 " pdb=" N MET B 308 " pdb=" CA MET B 308 " ideal model delta sigma weight residual 122.21 127.93 -5.72 1.62e+00 3.81e-01 1.25e+01 angle pdb=" C VAL B 309 " pdb=" N LYS B 310 " pdb=" CA LYS B 310 " ideal model delta sigma weight residual 122.40 127.49 -5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" N VAL B 373 " pdb=" CA VAL B 373 " pdb=" C VAL B 373 " ideal model delta sigma weight residual 111.77 108.19 3.58 1.04e+00 9.25e-01 1.19e+01 ... (remaining 4320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 1569 14.05 - 28.10: 161 28.10 - 42.15: 69 42.15 - 56.19: 12 56.19 - 70.24: 3 Dihedral angle restraints: 1814 sinusoidal: 611 harmonic: 1203 Sorted by residual: dihedral pdb=" CA LEU B 285 " pdb=" C LEU B 285 " pdb=" N ILE B 286 " pdb=" CA ILE B 286 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP A 72 " pdb=" C TRP A 72 " pdb=" N VAL A 73 " pdb=" CA VAL A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 212 " pdb=" C MET A 212 " pdb=" N TYR A 213 " pdb=" CA TYR A 213 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 401 0.049 - 0.098: 114 0.098 - 0.147: 19 0.147 - 0.195: 4 0.195 - 0.244: 2 Chirality restraints: 540 Sorted by residual: chirality pdb=" C10 HC3 A 501 " pdb=" C1 HC3 A 501 " pdb=" C5 HC3 A 501 " pdb=" C9 HC3 A 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.61 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA VAL B 377 " pdb=" N VAL B 377 " pdb=" C VAL B 377 " pdb=" CB VAL B 377 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 104 " pdb=" N GLU A 104 " pdb=" C GLU A 104 " pdb=" CB GLU A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 537 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 373 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C VAL B 373 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 373 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 374 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 433 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C MET B 433 " -0.044 2.00e-02 2.50e+03 pdb=" O MET B 433 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 434 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 11 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C ILE B 11 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B 11 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 12 " -0.011 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 62 2.64 - 3.21: 3488 3.21 - 3.77: 4769 3.77 - 4.34: 5981 4.34 - 4.90: 9342 Nonbonded interactions: 23642 Sorted by model distance: nonbonded pdb=" O GLN A 52 " pdb=" NE2 GLN A 52 " model vdw 2.079 2.520 nonbonded pdb=" O ARG A 53 " pdb=" OD1 ASN A 54 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 406 " pdb=" OG1 THR B 409 " model vdw 2.266 2.440 nonbonded pdb=" O PHE A 163 " pdb=" OG1 THR A 166 " model vdw 2.298 2.440 nonbonded pdb=" O PRO B 287 " pdb=" OG1 THR B 291 " model vdw 2.299 2.440 ... (remaining 23637 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 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: 0.330 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: 1.920 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 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 : 0.008 0.056 3163 Z= 0.542 Angle : 0.851 7.815 4325 Z= 0.500 Chirality : 0.048 0.244 540 Planarity : 0.005 0.034 522 Dihedral : 14.317 70.242 1036 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.11 % Favored : 92.65 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.35), residues: 408 helix: -2.04 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -4.52 (0.55), residues: 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.365 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1554 time to fit residues: 23.4531 Evaluate side-chains 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 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 50 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 3163 Z= 0.193 Angle : 0.701 7.446 4325 Z= 0.343 Chirality : 0.038 0.124 540 Planarity : 0.005 0.026 522 Dihedral : 5.105 51.371 445 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.62 % 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 (0.41), residues: 408 helix: 0.68 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -3.49 (0.61), residues: 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.1303 time to fit residues: 17.1849 Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0342 time to fit residues: 0.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 94 HIS ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3163 Z= 0.182 Angle : 0.688 10.780 4325 Z= 0.328 Chirality : 0.038 0.113 540 Planarity : 0.004 0.031 522 Dihedral : 4.870 52.796 445 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.28 % 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: 1.49 (0.43), residues: 408 helix: 1.85 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.04 (0.60), residues: 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.1307 time to fit residues: 16.2544 Evaluate side-chains 94 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0379 time to fit residues: 0.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 3163 Z= 0.201 Angle : 0.679 11.623 4325 Z= 0.329 Chirality : 0.038 0.117 540 Planarity : 0.004 0.033 522 Dihedral : 4.790 52.079 445 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 408 helix: 2.04 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -2.79 (0.63), residues: 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.1403 time to fit residues: 18.2007 Evaluate side-chains 92 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0325 time to fit residues: 0.7066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 99 HIS A 119 ASN A 170 GLN B 383 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 3163 Z= 0.188 Angle : 0.676 10.683 4325 Z= 0.326 Chirality : 0.038 0.148 540 Planarity : 0.004 0.035 522 Dihedral : 4.792 54.481 445 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.93 % 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: 1.87 (0.43), residues: 408 helix: 2.08 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.67 (0.64), residues: 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 104 average time/residue: 0.1309 time to fit residues: 17.0146 Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0316 time to fit residues: 0.7199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 0.0770 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3163 Z= 0.251 Angle : 0.716 11.687 4325 Z= 0.355 Chirality : 0.040 0.169 540 Planarity : 0.004 0.037 522 Dihedral : 4.893 58.022 445 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 4.59 % 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: 1.69 (0.43), residues: 408 helix: 1.94 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.99 (0.63), residues: 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1306 time to fit residues: 16.5969 Evaluate side-chains 97 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0347 time to fit residues: 1.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 3163 Z= 0.193 Angle : 0.705 12.118 4325 Z= 0.339 Chirality : 0.040 0.168 540 Planarity : 0.004 0.040 522 Dihedral : 4.831 57.469 445 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.43), residues: 408 helix: 2.10 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.69 (0.66), residues: 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.330 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 95 average time/residue: 0.1416 time to fit residues: 16.4180 Evaluate side-chains 88 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0379 time to fit residues: 0.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3163 Z= 0.193 Angle : 0.717 11.021 4325 Z= 0.347 Chirality : 0.041 0.168 540 Planarity : 0.005 0.042 522 Dihedral : 4.837 59.023 445 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.64 % 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: 2.00 (0.43), residues: 408 helix: 2.09 (0.29), residues: 335 sheet: None (None), residues: 0 loop : -2.53 (0.68), residues: 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.1235 time to fit residues: 14.9485 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0381 time to fit residues: 0.7824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 3163 Z= 0.224 Angle : 0.749 13.321 4325 Z= 0.363 Chirality : 0.042 0.186 540 Planarity : 0.005 0.041 522 Dihedral : 4.893 59.774 445 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.42), residues: 408 helix: 1.95 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.60 (0.65), residues: 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.335 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.1241 time to fit residues: 14.9086 Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0400 time to fit residues: 0.6413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 3163 Z= 0.215 Angle : 0.741 12.614 4325 Z= 0.358 Chirality : 0.041 0.171 540 Planarity : 0.005 0.042 522 Dihedral : 4.866 59.958 445 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.33 % 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: 1.88 (0.42), residues: 408 helix: 1.98 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.31 (0.68), residues: 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.411 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1184 time to fit residues: 14.2341 Evaluate side-chains 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.169845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133372 restraints weight = 6385.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.137781 restraints weight = 3453.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140726 restraints weight = 2410.295| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 3163 Z= 0.210 Angle : 0.760 13.251 4325 Z= 0.361 Chirality : 0.041 0.168 540 Planarity : 0.005 0.040 522 Dihedral : 4.836 57.910 445 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.66 % 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: 1.88 (0.42), residues: 408 helix: 1.96 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.21 (0.69), residues: 74 =============================================================================== Job complete usr+sys time: 1013.71 seconds wall clock time: 18 minutes 44.65 seconds (1124.65 seconds total)