Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:09:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/11_2022/6m49_30074_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/11_2022/6m49_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_30074/11_2022/6m49_30074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/11_2022/6m49_30074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/11_2022/6m49_30074_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m49_30074/11_2022/6m49_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None 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: 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: 2.32, per 1000 atoms: 0.75 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: 1.28 Conformation dependent library (CDL) restraints added in 482.0 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: 0.32 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: 1.38 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 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. 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: 0.000 Extract box with map and model: 1.890 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.353 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1495 time to fit residues: 22.6286 Evaluate side-chains 87 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4771 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 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 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: 0.6977 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 : 0.410 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.1220 time to fit residues: 16.1521 Evaluate side-chains 86 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0322 time to fit residues: 0.7630 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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: 0.6972 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3163 Z= 0.181 Angle : 0.685 10.720 4325 Z= 0.327 Chirality : 0.038 0.110 540 Planarity : 0.004 0.029 522 Dihedral : 4.868 52.557 445 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.95 % 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: 1.47 (0.43), residues: 408 helix: 1.84 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.03 (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: 9 poor density : 98 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.1213 time to fit residues: 15.1173 Evaluate side-chains 92 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0388 time to fit residues: 0.7752 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** 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: 0.7009 moved from start: 0.5180 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= 0.194 Angle : 0.683 11.647 4325 Z= 0.330 Chirality : 0.038 0.117 540 Planarity : 0.004 0.033 522 Dihedral : 4.790 52.506 445 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 1.76 (0.43), residues: 408 helix: 1.99 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.70 (0.63), residues: 77 *********************** 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 113 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.1297 time to fit residues: 16.6568 Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0302 time to fit residues: 0.8221 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 13 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 overall best weight: 0.5368 ------------------------------------------------------------------------------- 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 B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5627 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= 0.178 Angle : 0.666 10.744 4325 Z= 0.321 Chirality : 0.038 0.146 540 Planarity : 0.004 0.035 522 Dihedral : 4.743 54.182 445 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.43), residues: 408 helix: 2.06 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.67 (0.65), 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 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 100 average time/residue: 0.1233 time to fit residues: 15.5976 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0354 time to fit residues: 0.6499 ------------------------------------------------------------------------------- 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: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 3163 Z= 0.261 Angle : 0.714 10.420 4325 Z= 0.354 Chirality : 0.041 0.181 540 Planarity : 0.004 0.036 522 Dihedral : 4.902 58.125 445 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 4.92 % 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: 1.54 (0.42), residues: 408 helix: 1.86 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -3.04 (0.63), residues: 74 *********************** 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: 15 poor density : 92 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.1275 time to fit residues: 15.8580 Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0348 time to fit residues: 1.1576 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.0010 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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: 0.7047 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 3163 Z= 0.197 Angle : 0.741 11.199 4325 Z= 0.356 Chirality : 0.042 0.173 540 Planarity : 0.004 0.039 522 Dihedral : 4.767 56.820 445 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.77 (0.43), residues: 408 helix: 1.96 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.73 (0.67), 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 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.355 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.1286 time to fit residues: 15.7276 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0331 time to fit residues: 0.5932 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7036 moved from start: 0.6445 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= 0.198 Angle : 0.759 13.257 4325 Z= 0.363 Chirality : 0.042 0.178 540 Planarity : 0.005 0.041 522 Dihedral : 4.809 58.447 445 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 1.85 (0.43), residues: 408 helix: 1.99 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.56 (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 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.361 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.1174 time to fit residues: 14.2918 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0329 time to fit residues: 0.6468 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7060 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 3163 Z= 0.218 Angle : 0.751 12.462 4325 Z= 0.361 Chirality : 0.041 0.183 540 Planarity : 0.005 0.040 522 Dihedral : 4.796 59.022 445 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 1.78 (0.42), residues: 408 helix: 1.91 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -2.42 (0.69), 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 95 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.346 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.1169 time to fit residues: 13.7754 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0328 time to fit residues: 0.5685 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7032 moved from start: 0.6837 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= 0.206 Angle : 0.765 13.240 4325 Z= 0.365 Chirality : 0.042 0.178 540 Planarity : 0.005 0.039 522 Dihedral : 4.796 58.352 445 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 1.76 (0.42), residues: 408 helix: 1.88 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.24 (0.70), 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: 0 poor density : 96 time to evaluate : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1203 time to fit residues: 14.5377 Evaluate side-chains 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4790 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.170184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.132832 restraints weight = 6383.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137480 restraints weight = 3444.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.140571 restraints weight = 2386.141| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 3163 Z= 0.212 Angle : 0.770 13.251 4325 Z= 0.367 Chirality : 0.041 0.188 540 Planarity : 0.005 0.039 522 Dihedral : 4.740 55.828 445 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 1.84 (0.42), residues: 408 helix: 1.91 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -2.12 (0.71), residues: 74 =============================================================================== Job complete usr+sys time: 985.50 seconds wall clock time: 18 minutes 27.30 seconds (1107.30 seconds total)