Starting phenix.real_space_refine on Tue Sep 24 00:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/09_2024/7x90_33062_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/09_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_33062/09_2024/7x90_33062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/09_2024/7x90_33062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/09_2024/7x90_33062_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x90_33062/09_2024/7x90_33062_trim.cif" } 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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.98, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 1.71 Conformation dependent library (CDL) restraints added in 601.1 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: 0.62 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: 2.06 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: 0.00 - 1.07: 10928 1.07 - 2.14: 690 2.14 - 3.21: 42 3.21 - 4.27: 14 4.27 - 5.34: 4 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 2.450 nonbonded pdb=" OE2 GLU E 6 " pdb=" H GLY E 113 " model vdw 1.603 2.450 nonbonded pdb="HH21 ARG G 403 " pdb=" OE1 GLU G 406 " model vdw 1.651 2.450 nonbonded pdb=" O VAL G 503 " pdb="HE21 GLN G 506 " model vdw 1.671 2.450 nonbonded pdb=" O SER F 30 " pdb=" H GLY F 68 " model vdw 1.687 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.270 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: 0.240 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 18.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- 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 : 0.562 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: 0.3629 time to fit residues: 49.2047 Evaluate side-chains 81 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3384 Z= 0.269 Angle : 0.581 5.838 4600 Z= 0.306 Chirality : 0.042 0.147 502 Planarity : 0.004 0.036 595 Dihedral : 6.008 50.231 507 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % 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: -3.13 (0.37), residues: 414 helix: -2.09 (1.27), residues: 18 sheet: -0.43 (0.48), residues: 107 loop : -2.98 (0.31), residues: 289 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 0.019 0.001 PHE F 71 TYR 0.007 0.001 TYR G 453 ARG 0.003 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 90 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.512 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: 90 average time/residue: 0.3835 time to fit residues: 40.6232 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3384 Z= 0.182 Angle : 0.549 5.753 4600 Z= 0.286 Chirality : 0.042 0.146 502 Planarity : 0.004 0.040 595 Dihedral : 5.685 50.866 507 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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 (0.37), residues: 414 helix: -2.16 (1.25), residues: 18 sheet: -0.32 (0.47), residues: 113 loop : -2.86 (0.32), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.016 0.001 PHE F 71 TYR 0.007 0.001 TYR G 396 ARG 0.002 0.000 ARG E 87 *********************** 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 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.498 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: 94 average time/residue: 0.3996 time to fit residues: 43.6803 Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3102 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= 0.190 Angle : 0.535 5.673 4600 Z= 0.279 Chirality : 0.042 0.145 502 Planarity : 0.004 0.030 595 Dihedral : 5.520 50.984 507 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.04 % Favored : 86.71 % 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: -2.93 (0.37), residues: 414 helix: -2.09 (1.28), residues: 18 sheet: -0.63 (0.44), residues: 125 loop : -2.78 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.016 0.001 PHE G 400 TYR 0.006 0.001 TYR G 453 ARG 0.002 0.000 ARG G 454 *********************** 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 88 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.401 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: F 29 ILE cc_start: 0.8673 (mm) cc_final: 0.8462 (mm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3872 time to fit residues: 39.6740 Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3384 Z= 0.185 Angle : 0.539 5.448 4600 Z= 0.283 Chirality : 0.042 0.145 502 Planarity : 0.004 0.030 595 Dihedral : 5.458 51.134 507 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.11 % Favored : 88.65 % 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: -2.88 (0.38), residues: 414 helix: -2.07 (1.28), residues: 18 sheet: -0.69 (0.45), residues: 125 loop : -2.69 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.015 0.001 PHE G 400 TYR 0.007 0.001 TYR F 92 ARG 0.001 0.000 ARG E 87 *********************** 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 87 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.390 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: 87 average time/residue: 0.2891 time to fit residues: 29.4119 Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3333 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= 0.149 Angle : 0.524 5.432 4600 Z= 0.271 Chirality : 0.042 0.153 502 Planarity : 0.004 0.032 595 Dihedral : 5.349 51.712 507 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.87 % Favored : 88.89 % 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: -2.82 (0.38), residues: 414 helix: -2.03 (1.30), residues: 18 sheet: -0.72 (0.45), residues: 127 loop : -2.61 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.010 0.001 PHE G 400 TYR 0.008 0.001 TYR F 92 ARG 0.002 0.000 ARG E 87 *********************** 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 88 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.370 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: 88 average time/residue: 0.2895 time to fit residues: 29.9038 Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 0.1980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 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 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3384 Z= 0.150 Angle : 0.517 5.427 4600 Z= 0.268 Chirality : 0.042 0.146 502 Planarity : 0.004 0.032 595 Dihedral : 5.271 51.788 507 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.66 % Favored : 90.10 % 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: -2.86 (0.38), residues: 414 helix: -1.98 (1.31), residues: 18 sheet: -0.77 (0.44), residues: 129 loop : -2.64 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.010 0.001 PHE G 400 TYR 0.010 0.001 TYR F 87 ARG 0.001 0.000 ARG E 87 *********************** 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 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.520 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: 83 average time/residue: 0.3987 time to fit residues: 39.1399 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 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 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3592 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= 0.140 Angle : 0.502 5.479 4600 Z= 0.260 Chirality : 0.042 0.140 502 Planarity : 0.004 0.032 595 Dihedral : 5.204 52.042 507 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.63 % Favored : 89.13 % 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: -2.78 (0.38), residues: 414 helix: -1.99 (1.31), residues: 18 sheet: -0.69 (0.44), residues: 129 loop : -2.60 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.007 0.001 PHE G 374 TYR 0.008 0.001 TYR F 36 ARG 0.001 0.000 ARG E 87 *********************** 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 84 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.534 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: G 492 LEU cc_start: 0.8987 (mt) cc_final: 0.8393 (mp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3888 time to fit residues: 38.3430 Evaluate side-chains 66 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 0.4980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3612 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= 0.145 Angle : 0.500 5.489 4600 Z= 0.258 Chirality : 0.041 0.139 502 Planarity : 0.004 0.033 595 Dihedral : 5.167 51.884 507 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.73 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: -2.78 (0.38), residues: 414 helix: -1.99 (1.30), residues: 18 sheet: -0.76 (0.43), residues: 131 loop : -2.57 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.006 0.001 PHE F 71 TYR 0.007 0.001 TYR G 508 ARG 0.004 0.000 ARG E 87 *********************** 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 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.535 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: G 492 LEU cc_start: 0.9010 (mt) cc_final: 0.8417 (mp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3959 time to fit residues: 38.5695 Evaluate side-chains 66 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3384 Z= 0.139 Angle : 0.499 5.492 4600 Z= 0.258 Chirality : 0.042 0.145 502 Planarity : 0.004 0.033 595 Dihedral : 5.121 52.136 507 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.90 % Favored : 89.86 % 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: -2.66 (0.38), residues: 414 helix: -1.98 (1.31), residues: 18 sheet: -0.61 (0.44), residues: 129 loop : -2.51 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.008 0.001 PHE G 374 TYR 0.007 0.001 TYR G 508 ARG 0.003 0.000 ARG E 87 ********************** 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 84 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.518 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: G 492 LEU cc_start: 0.9007 (mt) cc_final: 0.8438 (mp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.4030 time to fit residues: 39.8930 Evaluate side-chains 66 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** 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 = 0.3381 r_free = 0.3381 target = 0.073446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059609 restraints weight = 35727.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063343 restraints weight = 15788.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065997 restraints weight = 8785.801| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3744 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= 0.145 Angle : 0.503 5.527 4600 Z= 0.260 Chirality : 0.041 0.140 502 Planarity : 0.004 0.033 595 Dihedral : 5.085 52.062 507 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.66 % Favored : 90.10 % 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: -2.68 (0.38), residues: 414 helix: -2.00 (1.30), residues: 18 sheet: -0.77 (0.43), residues: 133 loop : -2.46 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 35 HIS 0.003 0.001 HIS E 31 PHE 0.006 0.001 PHE F 98 TYR 0.005 0.001 TYR G 453 ARG 0.003 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.04 seconds wall clock time: 46 minutes 53.13 seconds (2813.13 seconds total)