Starting phenix.real_space_refine on Mon Nov 13 17:01:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcf_14629/11_2023/7zcf_14629.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.004 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2107 2.51 5 N 556 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E GLU 215": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.70 Number of scatterers: 3312 At special positions: 0 Unit cell: (65.786, 91.567, 90.678, 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 14 16.00 O 635 8.00 N 556 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 609.3 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 8.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.854A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.228A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.676A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.585A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.877A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.954A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.651A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.640A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.639A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.179A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188 removed outlier: 3.778A pdb=" N SER E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 132 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: 0.73 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1057 1.35 - 1.46: 899 1.46 - 1.58: 1423 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3395 Sorted by residual: bond pdb=" C PRO E 174 " pdb=" O PRO E 174 " ideal model delta sigma weight residual 1.235 1.268 -0.033 1.30e-02 5.92e+03 6.36e+00 bond pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 1.333 1.368 -0.036 1.57e-02 4.06e+03 5.19e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C SER E 228 " pdb=" N PRO E 229 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3390 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 98 106.90 - 113.67: 1758 113.67 - 120.43: 1272 120.43 - 127.20: 1455 127.20 - 133.97: 31 Bond angle restraints: 4614 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.47 -6.66 2.21e+00 2.05e-01 9.08e+00 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 118.46 -6.12 2.04e+00 2.40e-01 8.99e+00 angle pdb=" N GLN E 110 " pdb=" CA GLN E 110 " pdb=" C GLN E 110 " ideal model delta sigma weight residual 114.04 110.83 3.21 1.24e+00 6.50e-01 6.71e+00 angle pdb=" O PRO E 174 " pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 122.64 126.13 -3.49 1.35e+00 5.49e-01 6.68e+00 angle pdb=" N PRO C 337 " pdb=" CA PRO C 337 " pdb=" C PRO C 337 " ideal model delta sigma weight residual 114.68 112.10 2.58 1.04e+00 9.25e-01 6.13e+00 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1795 17.95 - 35.91: 160 35.91 - 53.86: 31 53.86 - 71.82: 4 71.82 - 89.77: 4 Dihedral angle restraints: 1994 sinusoidal: 769 harmonic: 1225 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.90 45.10 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 1991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 398 0.049 - 0.097: 80 0.097 - 0.146: 19 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 472 " pdb=" N ILE C 472 " pdb=" C ILE C 472 " pdb=" CB ILE C 472 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CB VAL E 116 " pdb=" CA VAL E 116 " pdb=" CG1 VAL E 116 " pdb=" CG2 VAL E 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 497 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 507 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 411 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 412 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 42 2.65 - 3.21: 2931 3.21 - 3.78: 4503 3.78 - 4.34: 6072 4.34 - 4.90: 10024 Nonbonded interactions: 23572 Sorted by model distance: nonbonded pdb=" OD1 ASN C 354 " pdb=" OG SER C 399 " model vdw 2.089 2.440 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR E 33 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASN C 331 " pdb=" N ILE C 332 " model vdw 2.228 2.520 nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.256 2.440 nonbonded pdb=" N GLN E 3 " pdb=" OG SER E 25 " model vdw 2.311 2.520 ... (remaining 23567 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 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: 2.960 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: 12.790 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 0.036 3395 Z= 0.177 Angle : 0.658 6.658 4614 Z= 0.371 Chirality : 0.045 0.243 500 Planarity : 0.005 0.054 597 Dihedral : 14.125 89.770 1202 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 0.56 % Allowed : 0.28 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.40), residues: 420 helix: -4.94 (0.47), residues: 8 sheet: -0.46 (0.55), residues: 104 loop : -2.12 (0.35), residues: 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.1601 time to fit residues: 13.9139 Evaluate side-chains 58 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0630 time to fit residues: 0.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3395 Z= 0.218 Angle : 0.646 7.009 4614 Z= 0.337 Chirality : 0.045 0.170 500 Planarity : 0.005 0.033 597 Dihedral : 5.193 22.479 472 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.86 % Favored : 82.14 % Rotamer: Outliers : 2.23 % Allowed : 12.85 % Favored : 84.92 % 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: -2.57 (0.41), residues: 420 helix: -4.89 (0.49), residues: 8 sheet: -1.17 (0.50), residues: 119 loop : -1.96 (0.37), residues: 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1326 time to fit residues: 13.5884 Evaluate side-chains 70 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0358 time to fit residues: 0.8469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3395 Z= 0.212 Angle : 0.649 6.860 4614 Z= 0.337 Chirality : 0.045 0.167 500 Planarity : 0.004 0.033 597 Dihedral : 5.194 23.960 472 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % Rotamer: Outliers : 3.35 % Allowed : 16.48 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.41), residues: 420 helix: -4.94 (0.46), residues: 8 sheet: -1.24 (0.49), residues: 121 loop : -1.94 (0.37), residues: 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.1322 time to fit residues: 11.5096 Evaluate side-chains 65 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0360 time to fit residues: 1.0062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 36 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3395 Z= 0.210 Angle : 0.647 6.879 4614 Z= 0.337 Chirality : 0.045 0.169 500 Planarity : 0.004 0.030 597 Dihedral : 5.292 23.790 472 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 3.07 % Allowed : 18.99 % Favored : 77.93 % 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: -2.59 (0.41), residues: 420 helix: -4.88 (0.51), residues: 8 sheet: -1.27 (0.50), residues: 115 loop : -1.93 (0.37), residues: 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.400 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.1459 time to fit residues: 12.4751 Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0426 time to fit residues: 1.0289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3395 Z= 0.293 Angle : 0.727 7.565 4614 Z= 0.386 Chirality : 0.047 0.203 500 Planarity : 0.005 0.035 597 Dihedral : 5.829 28.120 472 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.52 % Favored : 80.48 % Rotamer: Outliers : 1.96 % Allowed : 20.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.41), residues: 420 helix: -4.75 (0.62), residues: 8 sheet: -1.47 (0.48), residues: 125 loop : -2.11 (0.37), residues: 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.395 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 0.1379 time to fit residues: 10.3560 Evaluate side-chains 58 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0340 time to fit residues: 0.7643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3395 Z= 0.246 Angle : 0.699 6.934 4614 Z= 0.364 Chirality : 0.046 0.183 500 Planarity : 0.005 0.035 597 Dihedral : 5.606 27.170 472 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 2.51 % Allowed : 21.23 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.41), residues: 420 helix: -4.68 (0.68), residues: 8 sheet: -1.55 (0.49), residues: 123 loop : -2.18 (0.36), residues: 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.377 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1335 time to fit residues: 10.5426 Evaluate side-chains 62 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0447 time to fit residues: 0.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3395 Z= 0.207 Angle : 0.673 6.937 4614 Z= 0.349 Chirality : 0.045 0.188 500 Planarity : 0.004 0.033 597 Dihedral : 5.495 25.893 472 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.33 % Favored : 81.67 % Rotamer: Outliers : 1.96 % Allowed : 21.79 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.41), residues: 420 helix: -4.61 (0.75), residues: 8 sheet: -1.63 (0.49), residues: 122 loop : -2.09 (0.37), residues: 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1439 time to fit residues: 10.9271 Evaluate side-chains 60 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0424 time to fit residues: 0.8670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3395 Z= 0.254 Angle : 0.710 7.059 4614 Z= 0.369 Chirality : 0.045 0.183 500 Planarity : 0.005 0.035 597 Dihedral : 5.598 26.405 472 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 2.23 % Allowed : 21.79 % Favored : 75.98 % 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: -2.94 (0.41), residues: 420 helix: -4.62 (0.74), residues: 8 sheet: -1.67 (0.49), residues: 122 loop : -2.11 (0.37), residues: 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.401 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1427 time to fit residues: 9.9534 Evaluate side-chains 58 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0429 time to fit residues: 0.9225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3395 Z= 0.279 Angle : 0.723 7.137 4614 Z= 0.379 Chirality : 0.046 0.196 500 Planarity : 0.005 0.036 597 Dihedral : 5.809 27.140 472 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 1.40 % Allowed : 22.35 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.41), residues: 420 helix: -4.59 (0.76), residues: 8 sheet: -1.62 (0.50), residues: 124 loop : -2.19 (0.37), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.395 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1459 time to fit residues: 10.1573 Evaluate side-chains 55 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0511 time to fit residues: 0.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3395 Z= 0.223 Angle : 0.705 7.086 4614 Z= 0.364 Chirality : 0.046 0.185 500 Planarity : 0.005 0.034 597 Dihedral : 5.598 26.690 472 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.10 % Favored : 81.90 % Rotamer: Outliers : 0.56 % Allowed : 24.30 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.41), residues: 420 helix: -4.59 (0.76), residues: 8 sheet: -1.60 (0.51), residues: 120 loop : -2.16 (0.37), residues: 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.380 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1432 time to fit residues: 10.0028 Evaluate side-chains 54 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1889 time to fit residues: 0.9504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139537 restraints weight = 5829.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142355 restraints weight = 3672.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144350 restraints weight = 2637.028| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3395 Z= 0.255 Angle : 0.708 7.015 4614 Z= 0.368 Chirality : 0.045 0.186 500 Planarity : 0.005 0.036 597 Dihedral : 5.707 26.527 472 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 1.40 % Allowed : 23.74 % Favored : 74.86 % 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: -3.01 (0.41), residues: 420 helix: -4.53 (0.82), residues: 8 sheet: -1.53 (0.50), residues: 121 loop : -2.27 (0.37), residues: 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.69 seconds wall clock time: 24 minutes 37.00 seconds (1477.00 seconds total)