Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:50:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/04_2023/7tqd_26066_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5503 2.51 5 N 1511 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3999 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 484} Chain breaks: 4 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2961 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'peptide': 357, 'undetermined': 4} Modifications used: {'rna2p': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335, None: 5} Not linked: pdbres="ALA C 381 " pdbres="AMP C 401 " Not linked: pdbres="AMP C 401 " pdbres=" MG C 402 " Not linked: pdbres=" MG C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="ATP C 404 " Not linked: pdbres="ATP C 404 " pdbres="ADP C 405 " Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.24, per 1000 atoms: 0.60 Number of scatterers: 8690 At special positions: 0 Unit cell: (72.24, 100.8, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1640 8.00 N 1511 7.00 C 5503 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 6 sheets defined 35.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.546A pdb=" N MET A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.841A pdb=" N GLN A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 557 through 576 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 129 through 149 Processing helix chain 'B' and resid 179 through 186 Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 272 through 285 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 374 through 377 No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 557 through 576 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 85 through 99 removed outlier: 4.281A pdb=" N PHE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Proline residue: C 94 - end of helix Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 310 through 332 removed outlier: 3.589A pdb=" N ALA C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.919A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 593 through 597 removed outlier: 6.790A pdb=" N SER A 448 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE A 407 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 450 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 39 through 45 Processing sheet with id= C, first strand: chain 'B' and resid 357 through 360 removed outlier: 6.924A pdb=" N SER B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE B 212 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE B 194 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B 236 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 294 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 311 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA B 316 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 354 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 593 through 596 removed outlier: 6.932A pdb=" N SER B 448 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE B 407 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG B 450 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 104 through 107 removed outlier: 7.329A pdb=" N ASP C 121 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 70 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 123 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE C 72 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR C 125 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 74 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP C 71 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 125 through 127 353 hydrogen bonds defined for protein. 1017 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: 2.67 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2843 1.34 - 1.46: 1677 1.46 - 1.58: 4328 1.58 - 1.69: 8 1.69 - 1.81: 46 Bond restraints: 8902 Sorted by residual: bond pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.66e+00 bond pdb=" C4 ADP C 405 " pdb=" C5 ADP C 405 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4 AMP C 401 " pdb=" C5 AMP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CG PRO B 251 " pdb=" CD PRO B 251 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.10e+00 bond pdb=" C2' ADP C 405 " pdb=" C3' ADP C 405 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.31e-01 ... (remaining 8897 not shown) Histogram of bond angle deviations from ideal: 98.58 - 106.82: 326 106.82 - 115.05: 5348 115.05 - 123.29: 6016 123.29 - 131.53: 381 131.53 - 139.77: 43 Bond angle restraints: 12114 Sorted by residual: angle pdb=" CA TRP C 24 " pdb=" CB TRP C 24 " pdb=" CG TRP C 24 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.12e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" O ALA B 291 " ideal model delta sigma weight residual 119.13 121.16 -2.03 1.00e+00 1.00e+00 4.11e+00 angle pdb=" CA ALA B 291 " pdb=" C ALA B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 118.95 116.36 2.59 1.29e+00 6.01e-01 4.04e+00 angle pdb=" C ILE B 144 " pdb=" N ASP B 145 " pdb=" CA ASP B 145 " ideal model delta sigma weight residual 120.29 117.48 2.81 1.42e+00 4.96e-01 3.93e+00 angle pdb=" O1B ADP C 405 " pdb=" PB ADP C 405 " pdb=" O3B ADP C 405 " ideal model delta sigma weight residual 119.90 114.10 5.80 3.00e+00 1.11e-01 3.74e+00 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5225 34.65 - 69.30: 55 69.30 - 103.95: 0 103.95 - 138.60: 1 138.60 - 173.25: 2 Dihedral angle restraints: 5283 sinusoidal: 2112 harmonic: 3171 Sorted by residual: dihedral pdb=" O2A ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PA ADP C 405 " pdb=" PB ADP C 405 " ideal model delta sinusoidal sigma weight residual 300.00 126.75 173.25 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' AMP C 401 " pdb=" O5' AMP C 401 " pdb=" P AMP C 401 " pdb=" O3P AMP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.14 149.87 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP C 405 " pdb=" O3A ADP C 405 " pdb=" PB ADP C 405 " pdb=" PA ADP C 405 " ideal model delta sinusoidal sigma weight residual -60.00 59.27 -119.27 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 847 0.028 - 0.056: 325 0.056 - 0.084: 74 0.084 - 0.113: 66 0.113 - 0.141: 18 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C2' ADP C 405 " pdb=" C1' ADP C 405 " pdb=" C3' ADP C 405 " pdb=" O2' ADP C 405 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE C 127 " pdb=" N ILE C 127 " pdb=" C ILE C 127 " pdb=" CB ILE C 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1327 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 291 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ALA B 291 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA B 291 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 292 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 290 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ARG B 290 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG B 290 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 291 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 49 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 50 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " 0.027 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 20 2.55 - 3.14: 6211 3.14 - 3.72: 12782 3.72 - 4.31: 18375 4.31 - 4.90: 31337 Nonbonded interactions: 68725 Sorted by model distance: nonbonded pdb="MG MG C 403 " pdb=" O2B ATP C 404 " model vdw 1.960 2.170 nonbonded pdb=" OD2 ASP C 69 " pdb="MG MG C 402 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP C 71 " pdb="MG MG C 403 " model vdw 2.254 2.170 nonbonded pdb=" O ARG B 468 " pdb=" NZ LYS B 495 " model vdw 2.276 2.520 nonbonded pdb=" OD1 ASN B 374 " pdb=" NH2 ARG B 377 " model vdw 2.314 2.520 ... (remaining 68720 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 17.430 Check model and map are aligned: 0.160 Set scattering table: 0.070 Process input model: 27.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.003 0.031 8902 Z= 0.200 Angle : 0.520 7.302 12114 Z= 0.262 Chirality : 0.039 0.141 1330 Planarity : 0.004 0.049 1551 Dihedral : 11.717 173.252 3217 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.95 (0.26), residues: 1078 helix: 2.65 (0.26), residues: 402 sheet: 0.52 (0.34), residues: 232 loop : -1.28 (0.26), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.7058 time to fit residues: 280.9663 Evaluate side-chains 58 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 178 GLN C 8 ASN C 210 GLN C 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8902 Z= 0.196 Angle : 0.569 9.044 12114 Z= 0.272 Chirality : 0.039 0.165 1330 Planarity : 0.004 0.045 1551 Dihedral : 7.942 146.886 1193 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.98 (0.26), residues: 1078 helix: 2.69 (0.26), residues: 402 sheet: 0.53 (0.33), residues: 232 loop : -1.28 (0.26), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 1.089 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 78 average time/residue: 1.4210 time to fit residues: 118.3456 Evaluate side-chains 57 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1718 time to fit residues: 2.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 58 ASN B 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8902 Z= 0.207 Angle : 0.555 13.131 12114 Z= 0.265 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.036 1551 Dihedral : 6.736 115.770 1193 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.86 (0.25), residues: 1078 helix: 2.50 (0.26), residues: 404 sheet: 0.49 (0.33), residues: 232 loop : -1.29 (0.26), residues: 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 1.142 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 65 average time/residue: 1.3946 time to fit residues: 97.3434 Evaluate side-chains 54 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6727 time to fit residues: 2.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 8902 Z= 0.337 Angle : 0.624 8.268 12114 Z= 0.304 Chirality : 0.043 0.166 1330 Planarity : 0.005 0.043 1551 Dihedral : 6.429 95.622 1193 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.57 (0.25), residues: 1078 helix: 2.21 (0.26), residues: 402 sheet: 0.35 (0.33), residues: 236 loop : -1.41 (0.27), residues: 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 52 time to evaluate : 0.969 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 71 average time/residue: 1.1697 time to fit residues: 90.0803 Evaluate side-chains 55 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0809 time to fit residues: 1.5896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 149 GLN B 237 ASN C 227 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8902 Z= 0.203 Angle : 0.542 11.396 12114 Z= 0.259 Chirality : 0.040 0.153 1330 Planarity : 0.004 0.034 1551 Dihedral : 6.053 83.272 1193 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.72 (0.25), residues: 1078 helix: 2.34 (0.26), residues: 408 sheet: 0.35 (0.33), residues: 234 loop : -1.31 (0.27), residues: 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 1.181 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 64 average time/residue: 1.1306 time to fit residues: 78.7339 Evaluate side-chains 58 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0811 time to fit residues: 1.6372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 26 optimal weight: 0.0000 chunk 105 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 101 optimal weight: 0.8980 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 227 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8902 Z= 0.127 Angle : 0.519 11.925 12114 Z= 0.239 Chirality : 0.038 0.159 1330 Planarity : 0.003 0.031 1551 Dihedral : 5.675 76.353 1193 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.98 (0.26), residues: 1078 helix: 2.55 (0.26), residues: 408 sheet: 0.43 (0.33), residues: 236 loop : -1.14 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 1.026 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 1.2370 time to fit residues: 86.7551 Evaluate side-chains 56 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0808 time to fit residues: 1.5904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 41 optimal weight: 5.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8902 Z= 0.175 Angle : 0.531 12.479 12114 Z= 0.249 Chirality : 0.039 0.150 1330 Planarity : 0.004 0.032 1551 Dihedral : 5.609 78.019 1193 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.99 (0.26), residues: 1078 helix: 2.54 (0.26), residues: 408 sheet: 0.49 (0.33), residues: 235 loop : -1.15 (0.28), residues: 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 1.1516 time to fit residues: 74.0474 Evaluate side-chains 55 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0835 time to fit residues: 1.6485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8902 Z= 0.187 Angle : 0.541 11.808 12114 Z= 0.253 Chirality : 0.039 0.148 1330 Planarity : 0.004 0.031 1551 Dihedral : 5.561 80.788 1193 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.01 (0.26), residues: 1078 helix: 2.57 (0.26), residues: 408 sheet: 0.54 (0.34), residues: 231 loop : -1.16 (0.27), residues: 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 1.126 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 1.2056 time to fit residues: 81.2374 Evaluate side-chains 57 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0778 time to fit residues: 1.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8902 Z= 0.185 Angle : 0.537 12.451 12114 Z= 0.253 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.031 1551 Dihedral : 5.527 82.272 1193 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 1.00 (0.26), residues: 1078 helix: 2.52 (0.26), residues: 408 sheet: 0.54 (0.34), residues: 231 loop : -1.12 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 1.069 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 1.1567 time to fit residues: 70.5297 Evaluate side-chains 54 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 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 561 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8902 Z= 0.203 Angle : 0.547 12.170 12114 Z= 0.257 Chirality : 0.040 0.147 1330 Planarity : 0.004 0.031 1551 Dihedral : 5.519 83.551 1193 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.99 (0.26), residues: 1078 helix: 2.52 (0.26), residues: 407 sheet: 0.51 (0.33), residues: 231 loop : -1.11 (0.28), residues: 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 1.066 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 1.1556 time to fit residues: 69.1536 Evaluate side-chains 55 residues out of total 922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0808 time to fit residues: 1.6187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.0570 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN B 237 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076624 restraints weight = 16802.928| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.99 r_work: 0.3098 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8902 Z= 0.180 Angle : 0.535 14.317 12114 Z= 0.252 Chirality : 0.039 0.146 1330 Planarity : 0.004 0.031 1551 Dihedral : 5.460 85.515 1193 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.97 (0.26), residues: 1078 helix: 2.44 (0.26), residues: 409 sheet: 0.52 (0.33), residues: 231 loop : -1.08 (0.28), residues: 438 =============================================================================== Job complete usr+sys time: 2883.11 seconds wall clock time: 52 minutes 21.65 seconds (3141.65 seconds total)