Starting phenix.real_space_refine on Tue Feb 11 16:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_33062_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_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/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_33062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_33062.map" model { file = "/net/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_33062_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x90_33062/02_2025/7x90_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-5592/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: 3.37, per 1000 atoms: 0.52 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: 1.58 Conformation dependent library (CDL) restraints added in 612.9 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: 0.55 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: 2.00 Time building geometry restraints manager: 1.92 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.110 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.390 Find NCS groups from input model: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.522 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: 0.3681 time to fit residues: 50.0707 Evaluate side-chains 81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059209 restraints weight = 36084.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062816 restraints weight = 16104.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065344 restraints weight = 8923.783| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.502 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: E 46 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8788 (pt0) REVERT: G 389 ASP cc_start: 0.9239 (m-30) cc_final: 0.8960 (m-30) REVERT: G 467 ASP cc_start: 0.7232 (t0) cc_final: 0.6913 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3997 time to fit residues: 42.0457 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 37 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061720 restraints weight = 35659.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065556 restraints weight = 15807.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068157 restraints weight = 8703.453| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2715 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= 0.155 Angle : 0.543 5.782 4600 Z= 0.282 Chirality : 0.042 0.148 502 Planarity : 0.004 0.042 595 Dihedral : 5.649 51.471 507 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.63 % Favored : 89.13 % 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: -2.96 (0.37), residues: 414 helix: -2.11 (1.27), residues: 18 sheet: -0.37 (0.46), residues: 117 loop : -2.89 (0.32), residues: 279 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 0.006 0.001 TYR G 396 ARG 0.002 0.000 ARG G 454 *********************** 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 to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.543 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: E 46 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8761 (pt0) REVERT: E 102 MET cc_start: 0.8889 (mmm) cc_final: 0.8625 (mmm) REVERT: G 354 ASN cc_start: 0.9512 (m-40) cc_final: 0.9311 (m-40) REVERT: G 389 ASP cc_start: 0.9249 (m-30) cc_final: 0.8995 (m-30) REVERT: G 452 LEU cc_start: 0.9215 (mm) cc_final: 0.8986 (mm) REVERT: G 467 ASP cc_start: 0.7243 (t0) cc_final: 0.6879 (t0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.4186 time to fit residues: 45.8517 Evaluate side-chains 76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 6 GLN F 34 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059593 restraints weight = 37756.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063269 restraints weight = 16684.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.065801 restraints weight = 9237.415| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3384 Z= 0.228 Angle : 0.561 5.538 4600 Z= 0.294 Chirality : 0.042 0.143 502 Planarity : 0.004 0.030 595 Dihedral : 5.585 50.723 507 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.53 % Favored : 86.23 % 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: -2.99 (0.37), residues: 414 helix: -2.08 (1.28), residues: 18 sheet: -0.73 (0.44), residues: 127 loop : -2.80 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 35 HIS 0.004 0.002 HIS E 35 PHE 0.014 0.001 PHE F 71 TYR 0.007 0.001 TYR F 92 ARG 0.002 0.000 ARG E 87 *********************** 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 to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.543 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: E 46 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8815 (pt0) REVERT: E 102 MET cc_start: 0.8943 (mmm) cc_final: 0.8733 (mmm) REVERT: G 389 ASP cc_start: 0.9213 (m-30) cc_final: 0.8956 (m-30) REVERT: G 467 ASP cc_start: 0.7346 (t0) cc_final: 0.7041 (t0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4128 time to fit residues: 42.3799 Evaluate side-chains 77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 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 15 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** G 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056373 restraints weight = 37519.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059819 restraints weight = 17027.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062192 restraints weight = 9550.244| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.005 0.034 3384 Z= 0.324 Angle : 0.611 5.453 4600 Z= 0.322 Chirality : 0.042 0.142 502 Planarity : 0.005 0.045 595 Dihedral : 5.608 49.072 507 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.49 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: -3.36 (0.82), residues: 25 sheet: -0.77 (0.44), residues: 129 loop : -2.94 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 35 HIS 0.006 0.002 HIS E 31 PHE 0.022 0.002 PHE F 71 TYR 0.012 0.001 TYR G 396 ARG 0.002 0.000 ARG F 96 *********************** 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 88 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.577 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 59 HIS cc_start: 0.8547 (m90) cc_final: 0.8247 (m90) REVERT: F 17 ASP cc_start: 0.8557 (m-30) cc_final: 0.8345 (m-30) REVERT: G 389 ASP cc_start: 0.9156 (m-30) cc_final: 0.8904 (m-30) REVERT: G 467 ASP cc_start: 0.7424 (t0) cc_final: 0.7064 (t0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4218 time to fit residues: 43.4677 Evaluate side-chains 71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.0020 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 37 GLN G 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.058381 restraints weight = 36052.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062142 restraints weight = 15793.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064795 restraints weight = 8699.035| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3697 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= 0.162 Angle : 0.547 5.458 4600 Z= 0.284 Chirality : 0.042 0.146 502 Planarity : 0.004 0.033 595 Dihedral : 5.405 50.892 507 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.90 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: -2.91 (0.37), residues: 414 helix: -2.25 (1.23), residues: 18 sheet: -0.45 (0.46), residues: 119 loop : -2.80 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.009 0.001 PHE F 71 TYR 0.009 0.001 TYR G 508 ARG 0.002 0.000 ARG G 403 *********************** 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 90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.523 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: E 59 HIS cc_start: 0.8424 (m90) cc_final: 0.8093 (m90) REVERT: F 17 ASP cc_start: 0.8595 (m-30) cc_final: 0.8366 (m-30) REVERT: G 345 THR cc_start: 0.9102 (m) cc_final: 0.8493 (m) REVERT: G 354 ASN cc_start: 0.9549 (m-40) cc_final: 0.9333 (m-40) REVERT: G 389 ASP cc_start: 0.9140 (m-30) cc_final: 0.8900 (m-30) REVERT: G 452 LEU cc_start: 0.9241 (mm) cc_final: 0.8976 (mm) REVERT: G 467 ASP cc_start: 0.7386 (t0) cc_final: 0.7074 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4027 time to fit residues: 43.0126 Evaluate side-chains 71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN G 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.072764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059204 restraints weight = 35397.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062953 restraints weight = 15509.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065616 restraints weight = 8548.239| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3792 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= 0.146 Angle : 0.521 5.480 4600 Z= 0.270 Chirality : 0.042 0.144 502 Planarity : 0.004 0.033 595 Dihedral : 5.291 51.684 507 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.18 % Favored : 90.58 % 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: -2.90 (0.37), residues: 414 helix: -2.06 (1.28), residues: 18 sheet: -0.49 (0.46), residues: 117 loop : -2.76 (0.32), residues: 279 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 0.008 0.001 PHE G 400 TYR 0.006 0.001 TYR G 453 ARG 0.002 0.000 ARG G 403 *********************** 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 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.556 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: E 59 HIS cc_start: 0.8430 (m90) cc_final: 0.8085 (m90) REVERT: G 345 THR cc_start: 0.9089 (m) cc_final: 0.8477 (m) REVERT: G 354 ASN cc_start: 0.9555 (m-40) cc_final: 0.9352 (m-40) REVERT: G 389 ASP cc_start: 0.9177 (m-30) cc_final: 0.8949 (m-30) REVERT: G 452 LEU cc_start: 0.9222 (mm) cc_final: 0.8944 (mm) REVERT: G 467 ASP cc_start: 0.7415 (t0) cc_final: 0.7152 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3931 time to fit residues: 39.0317 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.071431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057972 restraints weight = 36787.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061645 restraints weight = 16196.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064253 restraints weight = 8941.473| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3384 Z= 0.203 Angle : 0.535 5.511 4600 Z= 0.278 Chirality : 0.042 0.163 502 Planarity : 0.004 0.033 595 Dihedral : 5.267 50.712 507 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.11 % Favored : 88.65 % 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: -2.91 (0.38), residues: 414 helix: -2.11 (1.27), residues: 18 sheet: -0.67 (0.44), residues: 131 loop : -2.77 (0.33), residues: 265 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 0.011 0.001 PHE F 71 TYR 0.011 0.001 TYR F 87 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 to be fit. rotamer outliers: 0 poor density : 84 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: E 59 HIS cc_start: 0.8541 (m90) cc_final: 0.8130 (m90) REVERT: G 345 THR cc_start: 0.9114 (m) cc_final: 0.8497 (m) REVERT: G 354 ASN cc_start: 0.9561 (m-40) cc_final: 0.9357 (m-40) REVERT: G 389 ASP cc_start: 0.9153 (m-30) cc_final: 0.8925 (m-30) REVERT: G 467 ASP cc_start: 0.7387 (t0) cc_final: 0.7110 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3878 time to fit residues: 38.5179 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.4702 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057861 restraints weight = 36731.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061575 restraints weight = 16254.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064221 restraints weight = 8983.112| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3384 Z= 0.177 Angle : 0.524 5.522 4600 Z= 0.271 Chirality : 0.042 0.140 502 Planarity : 0.004 0.033 595 Dihedral : 5.246 51.034 507 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.11 % Favored : 88.65 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.38), residues: 414 helix: -2.09 (1.27), residues: 18 sheet: -0.73 (0.44), residues: 135 loop : -2.76 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.008 0.001 PHE F 71 TYR 0.006 0.001 TYR G 453 ARG 0.002 0.000 ARG G 454 *********************** 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 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.617 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: E 59 HIS cc_start: 0.8580 (m90) cc_final: 0.8106 (m90) REVERT: G 345 THR cc_start: 0.9131 (m) cc_final: 0.8518 (m) REVERT: G 354 ASN cc_start: 0.9552 (m-40) cc_final: 0.9349 (m-40) REVERT: G 389 ASP cc_start: 0.9154 (m-30) cc_final: 0.8924 (m-30) REVERT: G 467 ASP cc_start: 0.7394 (t0) cc_final: 0.7112 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3890 time to fit residues: 37.8912 Evaluate side-chains 69 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055852 restraints weight = 36897.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.059512 restraints weight = 16363.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062168 restraints weight = 9085.634| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4216 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= 0.234 Angle : 0.551 5.564 4600 Z= 0.287 Chirality : 0.041 0.136 502 Planarity : 0.004 0.040 595 Dihedral : 5.298 50.469 507 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.80 % Favored : 86.96 % 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: -2.88 (0.38), residues: 414 helix: -2.09 (1.22), residues: 18 sheet: -0.54 (0.45), residues: 130 loop : -2.81 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.014 0.001 PHE F 71 TYR 0.009 0.001 TYR F 86 ARG 0.002 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 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.508 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: G 345 THR cc_start: 0.9150 (m) cc_final: 0.8695 (m) REVERT: G 354 ASN cc_start: 0.9559 (m-40) cc_final: 0.9353 (m-40) REVERT: G 389 ASP cc_start: 0.9163 (m-30) cc_final: 0.8945 (m-30) REVERT: G 467 ASP cc_start: 0.7403 (t0) cc_final: 0.7114 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3919 time to fit residues: 37.7422 Evaluate side-chains 66 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061937 restraints weight = 34749.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065556 restraints weight = 15052.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068058 restraints weight = 8146.682| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3384 Z= 0.168 Angle : 0.530 5.541 4600 Z= 0.276 Chirality : 0.042 0.141 502 Planarity : 0.004 0.039 595 Dihedral : 5.262 51.286 507 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.90 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.38), residues: 414 helix: -2.01 (1.24), residues: 18 sheet: -0.65 (0.44), residues: 135 loop : -2.77 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.011 0.001 PHE E 95 TYR 0.007 0.001 TYR G 453 ARG 0.002 0.000 ARG G 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.37 seconds wall clock time: 50 minutes 37.34 seconds (3037.34 seconds total)