Starting phenix.real_space_refine on Mon Mar 11 00:56:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/03_2024/7x90_33062_trim.pdb" } resolution = 4.2 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 16 5.16 5 C 2092 2.51 5 N 560 2.21 5 O 633 1.98 5 H 3140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 389": "OD1" <-> "OD2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6441 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1816 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1609 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.56, per 1000 atoms: 0.55 Number of scatterers: 6441 At special positions: 0 Unit cell: (98.651, 71.294, 71.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 O 633 8.00 N 560 7.00 C 2092 6.00 H 3140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 693.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 5.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 366 through 371 removed outlier: 3.624A pdb=" N SER G 371 " --> pdb=" O VAL G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.571A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.779A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.664A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 38 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 356 through 358 removed outlier: 3.779A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 74 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3140 1.03 - 1.23: 18 1.23 - 1.43: 1484 1.43 - 1.62: 1862 1.62 - 1.82: 20 Bond restraints: 6524 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C THR F 94 " pdb=" N PRO F 95 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.57e+00 ... (remaining 6519 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.26: 173 107.26 - 113.94: 7421 113.94 - 120.61: 2226 120.61 - 127.28: 1822 127.28 - 133.95: 36 Bond angle restraints: 11678 Sorted by residual: angle pdb=" C SER F 30 " pdb=" CA SER F 30 " pdb=" CB SER F 30 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.99e+00 2.53e-01 7.21e+00 angle pdb=" N SER F 30 " pdb=" CA SER F 30 " pdb=" C SER F 30 " ideal model delta sigma weight residual 110.80 106.54 4.26 2.13e+00 2.20e-01 3.99e+00 angle pdb=" CA SER F 30 " pdb=" C SER F 30 " pdb=" N ASN F 31 " ideal model delta sigma weight residual 116.84 119.83 -2.99 1.71e+00 3.42e-01 3.06e+00 angle pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" C THR F 94 " ideal model delta sigma weight residual 109.81 113.40 -3.59 2.21e+00 2.05e-01 2.63e+00 angle pdb=" C TYR G 508 " pdb=" N ARG G 509 " pdb=" CA ARG G 509 " ideal model delta sigma weight residual 122.30 120.12 2.18 1.35e+00 5.49e-01 2.62e+00 ... (remaining 11673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 2768 14.68 - 29.36: 250 29.36 - 44.04: 116 44.04 - 58.72: 43 58.72 - 73.39: 5 Dihedral angle restraints: 3182 sinusoidal: 1702 harmonic: 1480 Sorted by residual: dihedral pdb=" CA CYS G 336 " pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " ideal model delta sinusoidal sigma weight residual -73.00 -7.14 -65.86 1 2.00e+01 2.50e-03 1.42e+01 dihedral pdb=" CA GLU G 516 " pdb=" C GLU G 516 " pdb=" N LEU G 517 " pdb=" CA LEU G 517 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.36 -27.64 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 3179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 329 0.034 - 0.068: 119 0.068 - 0.101: 39 0.101 - 0.135: 14 0.135 - 0.169: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA ILE G 434 " pdb=" N ILE G 434 " pdb=" C ILE G 434 " pdb=" CB ILE G 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL G 511 " pdb=" N VAL G 511 " pdb=" C VAL G 511 " pdb=" CB VAL G 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 499 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 32 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO E 33 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 33 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 33 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 506 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 507 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 507 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 508 " -0.000 2.00e-02 2.50e+03 5.50e-03 9.07e-01 pdb=" CG TYR G 508 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR G 508 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 508 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G 508 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 508 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 508 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR G 508 " -0.001 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 380 2.18 - 2.78: 12634 2.78 - 3.39: 16304 3.39 - 3.99: 21120 3.99 - 4.60: 31957 Nonbonded interactions: 82395 Sorted by model distance: nonbonded pdb=" O GLN F 79 " pdb=" H GLU F 81 " model vdw 1.575 1.850 nonbonded pdb=" OE2 GLU E 6 " pdb=" H GLY E 113 " model vdw 1.603 1.850 nonbonded pdb="HH21 ARG G 403 " pdb=" OE1 GLU G 406 " model vdw 1.651 1.850 nonbonded pdb=" O VAL G 503 " pdb="HE21 GLN G 506 " model vdw 1.671 1.850 nonbonded pdb=" O SER F 30 " pdb=" H GLY F 68 " model vdw 1.687 1.850 ... (remaining 82390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.100 Extract box with map and model: 1.220 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.970 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 0.033 3384 Z= 0.190 Angle : 0.579 5.343 4600 Z= 0.304 Chirality : 0.042 0.169 502 Planarity : 0.003 0.033 595 Dihedral : 13.963 73.394 1235 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -3.08 (0.37), residues: 414 helix: -3.48 (1.39), residues: 12 sheet: -0.39 (0.47), residues: 111 loop : -2.90 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.005 0.001 PHE G 456 TYR 0.012 0.001 TYR G 508 ARG 0.002 0.000 ARG G 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 HIS cc_start: 0.8566 (m90) cc_final: 0.8193 (m170) REVERT: E 99 LEU cc_start: 0.8952 (mt) cc_final: 0.8632 (mt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3914 time to fit residues: 53.1200 Evaluate side-chains 81 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3384 Z= 0.308 Angle : 0.592 5.836 4600 Z= 0.311 Chirality : 0.041 0.148 502 Planarity : 0.004 0.030 595 Dihedral : 6.108 49.753 507 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.29 % Favored : 86.47 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: -3.23 (0.37), residues: 414 helix: -2.22 (1.23), residues: 18 sheet: -0.58 (0.46), residues: 114 loop : -3.05 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 353 HIS 0.006 0.002 HIS E 31 PHE 0.021 0.002 PHE F 71 TYR 0.007 0.001 TYR G 453 ARG 0.002 0.000 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.4013 time to fit residues: 41.1767 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3384 Z= 0.284 Angle : 0.582 5.698 4600 Z= 0.304 Chirality : 0.041 0.146 502 Planarity : 0.004 0.031 595 Dihedral : 5.961 49.458 507 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -3.20 (0.36), residues: 414 helix: -2.16 (1.19), residues: 18 sheet: -0.43 (0.47), residues: 113 loop : -3.09 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 35 HIS 0.006 0.001 HIS E 31 PHE 0.021 0.001 PHE F 71 TYR 0.012 0.001 TYR G 396 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3445 time to fit residues: 36.9927 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3384 Z= 0.167 Angle : 0.541 5.450 4600 Z= 0.282 Chirality : 0.042 0.148 502 Planarity : 0.004 0.031 595 Dihedral : 5.700 51.151 507 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.87 % Favored : 88.65 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -3.03 (0.38), residues: 414 helix: -2.10 (1.26), residues: 18 sheet: -0.55 (0.45), residues: 124 loop : -2.92 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.011 0.001 PHE F 71 TYR 0.009 0.001 TYR F 92 ARG 0.001 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3707 time to fit residues: 40.1859 Evaluate side-chains 78 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3384 Z= 0.184 Angle : 0.527 5.256 4600 Z= 0.273 Chirality : 0.041 0.143 502 Planarity : 0.004 0.029 595 Dihedral : 5.531 51.151 507 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.35 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -2.99 (0.37), residues: 414 helix: -2.20 (1.23), residues: 18 sheet: -0.54 (0.45), residues: 125 loop : -2.89 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.010 0.001 PHE F 71 TYR 0.006 0.001 TYR F 92 ARG 0.001 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4335 time to fit residues: 44.4368 Evaluate side-chains 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3384 Z= 0.268 Angle : 0.569 5.255 4600 Z= 0.295 Chirality : 0.041 0.139 502 Planarity : 0.004 0.037 595 Dihedral : 5.540 50.081 507 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.56 % Favored : 87.20 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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 (0.37), residues: 414 helix: -3.30 (0.82), residues: 25 sheet: -0.27 (0.47), residues: 118 loop : -2.88 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.017 0.001 PHE F 71 TYR 0.010 0.001 TYR G 396 ARG 0.001 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3572 time to fit residues: 34.9300 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN G 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3384 Z= 0.151 Angle : 0.528 5.304 4600 Z= 0.271 Chirality : 0.042 0.143 502 Planarity : 0.004 0.033 595 Dihedral : 5.403 51.529 507 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.42 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.92 (0.38), residues: 414 helix: -2.39 (1.18), residues: 18 sheet: -0.61 (0.46), residues: 126 loop : -2.76 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.007 0.001 PHE F 71 TYR 0.006 0.001 TYR F 86 ARG 0.002 0.000 ARG F 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3730 time to fit residues: 39.5550 Evaluate side-chains 71 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3384 Z= 0.135 Angle : 0.513 5.304 4600 Z= 0.265 Chirality : 0.042 0.171 502 Planarity : 0.004 0.034 595 Dihedral : 5.259 52.154 507 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.66 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 (0.38), residues: 414 helix: -2.39 (1.15), residues: 18 sheet: -0.57 (0.45), residues: 126 loop : -2.69 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.005 0.001 PHE G 497 TYR 0.010 0.001 TYR G 508 ARG 0.001 0.000 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.4207 time to fit residues: 43.3221 Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3384 Z= 0.145 Angle : 0.524 5.341 4600 Z= 0.268 Chirality : 0.042 0.143 502 Planarity : 0.004 0.033 595 Dihedral : 5.247 52.201 507 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.14 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 (0.38), residues: 414 helix: -2.26 (1.19), residues: 18 sheet: -0.63 (0.45), residues: 121 loop : -2.63 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.029 0.001 PHE G 400 TYR 0.007 0.001 TYR G 508 ARG 0.002 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3287 time to fit residues: 33.2815 Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3384 Z= 0.251 Angle : 0.552 5.522 4600 Z= 0.288 Chirality : 0.041 0.148 502 Planarity : 0.004 0.034 595 Dihedral : 5.326 50.768 507 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.99 (0.38), residues: 414 helix: -2.37 (1.17), residues: 18 sheet: -0.68 (0.44), residues: 125 loop : -2.79 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.013 0.001 PHE F 71 TYR 0.009 0.001 TYR G 396 ARG 0.003 0.000 ARG F 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3325 time to fit residues: 32.4202 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060151 restraints weight = 35966.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063851 restraints weight = 16265.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066409 restraints weight = 9002.373| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3384 Z= 0.147 Angle : 0.512 5.397 4600 Z= 0.266 Chirality : 0.042 0.141 502 Planarity : 0.004 0.034 595 Dihedral : 5.231 51.797 507 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.14 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.38), residues: 414 helix: -2.23 (1.23), residues: 18 sheet: -0.63 (0.44), residues: 126 loop : -2.66 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.011 0.001 PHE G 374 TYR 0.007 0.001 TYR G 508 ARG 0.001 0.000 ARG G 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.37 seconds wall clock time: 45 minutes 18.21 seconds (2718.21 seconds total)