Starting phenix.real_space_refine on Tue Feb 13 16:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/02_2024/6nf4_9360.pdb" } resolution = 2.98 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 4630 2.51 5 N 1084 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 53": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ARG 584": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6960 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3347 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 13, 'TRANS': 407} Chain breaks: 4 Chain: "B" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3347 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 13, 'TRANS': 407} Chain breaks: 4 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'CLR': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'CLR': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.36, per 1000 atoms: 0.63 Number of scatterers: 6960 At special positions: 0 Unit cell: (85.49, 77.25, 72.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1180 8.00 N 1084 7.00 C 4630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.517A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 109 removed outlier: 3.648A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 150 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 190 through 213 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 249 through 283 Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 304 through 330 Processing helix chain 'A' and resid 334 through 367 removed outlier: 3.674A pdb=" N ALA A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.571A pdb=" N THR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 442 removed outlier: 3.707A pdb=" N TYR A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 537 Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 540 through 545 removed outlier: 4.025A pdb=" N TYR A 543 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 584 Proline residue: A 566 - end of helix Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.517A pdb=" N ALA B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 109 removed outlier: 3.648A pdb=" N LEU B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 150 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 190 through 213 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 249 through 283 Proline residue: B 263 - end of helix Processing helix chain 'B' and resid 304 through 330 Processing helix chain 'B' and resid 334 through 367 removed outlier: 3.674A pdb=" N ALA B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.571A pdb=" N THR B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 442 removed outlier: 3.707A pdb=" N TYR B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 537 Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 540 through 545 removed outlier: 4.025A pdb=" N TYR B 543 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 584 Proline residue: B 566 - end of helix 568 hydrogen bonds defined for protein. 1692 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: 1.98 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1170 1.33 - 1.45: 1864 1.45 - 1.57: 4006 1.57 - 1.69: 2 1.69 - 1.81: 110 Bond restraints: 7152 Sorted by residual: bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 604 " pdb=" OAH Y01 B 604 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A 603 " pdb=" OAH Y01 A 603 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A 604 " pdb=" OAH Y01 A 604 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 94.82 - 102.70: 76 102.70 - 110.58: 2208 110.58 - 118.46: 3506 118.46 - 126.33: 3806 126.33 - 134.21: 144 Bond angle restraints: 9740 Sorted by residual: angle pdb=" CA GLU A 550 " pdb=" CB GLU A 550 " pdb=" CG GLU A 550 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA GLU B 550 " pdb=" CB GLU B 550 " pdb=" CG GLU B 550 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C ILE A 186 " pdb=" N LYS A 187 " pdb=" CA LYS A 187 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ILE B 186 " pdb=" N LYS B 187 " pdb=" CA LYS B 187 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ARG A 540 " pdb=" CA ARG A 540 " pdb=" CB ARG A 540 " ideal model delta sigma weight residual 111.20 108.80 2.40 7.10e-01 1.98e+00 1.14e+01 ... (remaining 9735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4202 17.88 - 35.75: 274 35.75 - 53.63: 60 53.63 - 71.51: 12 71.51 - 89.38: 10 Dihedral angle restraints: 4558 sinusoidal: 2102 harmonic: 2456 Sorted by residual: dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLU B 548 " pdb=" C GLU B 548 " pdb=" N ASN B 549 " pdb=" CA ASN B 549 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA MET A 371 " pdb=" C MET A 371 " pdb=" N ASP A 372 " pdb=" CA ASP A 372 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 946 0.077 - 0.153: 148 0.153 - 0.230: 18 0.230 - 0.307: 14 0.307 - 0.383: 8 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CBG Y01 B 604 " pdb=" CAQ Y01 B 604 " pdb=" CBD Y01 B 604 " pdb=" CBI Y01 B 604 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 1131 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 170 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C HIS B 170 " 0.066 2.00e-02 2.50e+03 pdb=" O HIS B 170 " -0.025 2.00e-02 2.50e+03 pdb=" N THR B 171 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 170 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C HIS A 170 " -0.066 2.00e-02 2.50e+03 pdb=" O HIS A 170 " 0.025 2.00e-02 2.50e+03 pdb=" N THR A 171 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 171 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C THR B 171 " -0.057 2.00e-02 2.50e+03 pdb=" O THR B 171 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 172 " 0.019 2.00e-02 2.50e+03 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2448 2.88 - 3.39: 6908 3.39 - 3.89: 11691 3.89 - 4.40: 12724 4.40 - 4.90: 22596 Nonbonded interactions: 56367 Sorted by model distance: nonbonded pdb=" O ARG B 379 " pdb=" OG1 THR B 383 " model vdw 2.379 2.440 nonbonded pdb=" O ARG A 379 " pdb=" OG1 THR A 383 " model vdw 2.379 2.440 nonbonded pdb=" OG1 THR B 216 " pdb=" ND2 ASN B 562 " model vdw 2.393 2.520 nonbonded pdb=" OG1 THR A 216 " pdb=" ND2 ASN A 562 " model vdw 2.393 2.520 nonbonded pdb=" O GLN A 515 " pdb=" ND2 ASN A 519 " model vdw 2.408 2.520 ... (remaining 56362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.120 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.009 0.094 7152 Z= 0.567 Angle : 1.092 9.263 9740 Z= 0.552 Chirality : 0.070 0.383 1134 Planarity : 0.007 0.043 1134 Dihedral : 13.593 89.384 2974 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.27 % Allowed : 1.63 % Favored : 98.10 % 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: 0.16 (0.27), residues: 822 helix: 0.66 (0.17), residues: 696 sheet: None (None), residues: 0 loop : -2.68 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 417 HIS 0.006 0.001 HIS B 574 PHE 0.025 0.003 PHE B 525 TYR 0.018 0.003 TYR B 189 ARG 0.007 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 0.815 Fit side-chains REVERT: A 429 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7966 (pp20) REVERT: B 429 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7964 (pp20) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 1.4516 time to fit residues: 224.2545 Evaluate side-chains 100 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.0000 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN B 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7152 Z= 0.168 Angle : 0.541 6.940 9740 Z= 0.281 Chirality : 0.038 0.144 1134 Planarity : 0.004 0.034 1134 Dihedral : 9.704 55.448 1460 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.52 % Allowed : 8.67 % Favored : 87.80 % 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: 2.75 (0.29), residues: 822 helix: 2.52 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -2.60 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 417 HIS 0.002 0.001 HIS A 176 PHE 0.017 0.002 PHE B 525 TYR 0.010 0.001 TYR B 189 ARG 0.005 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.739 Fit side-chains REVERT: A 364 TYR cc_start: 0.8656 (m-10) cc_final: 0.8310 (m-80) REVERT: B 364 TYR cc_start: 0.8656 (m-10) cc_final: 0.8310 (m-80) outliers start: 26 outliers final: 8 residues processed: 132 average time/residue: 1.1695 time to fit residues: 162.8829 Evaluate side-chains 112 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 562 ASN B 174 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7152 Z= 0.163 Angle : 0.518 8.710 9740 Z= 0.265 Chirality : 0.037 0.142 1134 Planarity : 0.004 0.037 1134 Dihedral : 9.028 54.449 1460 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.07 % Allowed : 10.57 % Favored : 85.37 % 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: 3.56 (0.30), residues: 822 helix: 3.06 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -2.77 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 179 HIS 0.003 0.001 HIS B 327 PHE 0.015 0.001 PHE B 202 TYR 0.013 0.001 TYR B 442 ARG 0.003 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.770 Fit side-chains REVERT: A 391 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8275 (mp) REVERT: B 391 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8276 (mp) outliers start: 30 outliers final: 10 residues processed: 120 average time/residue: 1.2823 time to fit residues: 161.7276 Evaluate side-chains 118 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7152 Z= 0.172 Angle : 0.534 9.229 9740 Z= 0.268 Chirality : 0.037 0.148 1134 Planarity : 0.004 0.040 1134 Dihedral : 8.691 56.788 1460 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.25 % Allowed : 13.55 % Favored : 83.20 % 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: 3.84 (0.30), residues: 822 helix: 3.29 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -3.01 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 280 HIS 0.002 0.001 HIS B 574 PHE 0.016 0.001 PHE A 525 TYR 0.008 0.001 TYR B 189 ARG 0.006 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.758 Fit side-chains REVERT: A 220 MET cc_start: 0.6605 (mtp) cc_final: 0.6399 (ttm) REVERT: A 391 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 220 MET cc_start: 0.6609 (mtp) cc_final: 0.6399 (ttm) REVERT: B 391 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8300 (mp) outliers start: 24 outliers final: 6 residues processed: 116 average time/residue: 1.3402 time to fit residues: 163.1169 Evaluate side-chains 112 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 562 ASN B 174 GLN B 410 GLN B 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7152 Z= 0.171 Angle : 0.517 8.933 9740 Z= 0.257 Chirality : 0.037 0.154 1134 Planarity : 0.004 0.037 1134 Dihedral : 8.291 55.106 1460 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 15.04 % Favored : 82.25 % 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: 4.01 (0.30), residues: 822 helix: 3.42 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.95 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 280 HIS 0.002 0.001 HIS B 574 PHE 0.016 0.001 PHE A 525 TYR 0.012 0.001 TYR B 442 ARG 0.004 0.001 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.797 Fit side-chains REVERT: A 267 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 391 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 267 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: B 391 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8287 (mp) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 1.2881 time to fit residues: 153.2265 Evaluate side-chains 117 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7152 Z= 0.167 Angle : 0.509 8.825 9740 Z= 0.253 Chirality : 0.036 0.160 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.029 54.527 1460 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.85 % Allowed : 15.85 % Favored : 81.30 % 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: 4.09 (0.30), residues: 822 helix: 3.46 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -2.88 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 280 HIS 0.002 0.001 HIS A 170 PHE 0.016 0.001 PHE A 525 TYR 0.007 0.001 TYR A 189 ARG 0.003 0.000 ARG B 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.781 Fit side-chains REVERT: A 391 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 391 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (mp) outliers start: 21 outliers final: 14 residues processed: 122 average time/residue: 1.2024 time to fit residues: 154.6115 Evaluate side-chains 126 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7152 Z= 0.135 Angle : 0.490 8.405 9740 Z= 0.244 Chirality : 0.036 0.157 1134 Planarity : 0.003 0.038 1134 Dihedral : 7.732 55.881 1460 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.17 % Allowed : 16.26 % Favored : 81.57 % 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: 4.33 (0.30), residues: 822 helix: 3.71 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.79 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 280 HIS 0.003 0.000 HIS B 176 PHE 0.015 0.001 PHE B 525 TYR 0.010 0.001 TYR B 442 ARG 0.002 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.756 Fit side-chains REVERT: A 220 MET cc_start: 0.6720 (mtp) cc_final: 0.6512 (mtm) REVERT: A 341 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7574 (ttp) REVERT: A 391 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 220 MET cc_start: 0.6722 (mtp) cc_final: 0.6514 (mtm) REVERT: B 341 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7574 (ttp) REVERT: B 391 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 16 outliers final: 8 residues processed: 118 average time/residue: 1.1866 time to fit residues: 147.5126 Evaluate side-chains 124 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 562 ASN B 174 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7152 Z= 0.220 Angle : 0.532 9.253 9740 Z= 0.263 Chirality : 0.038 0.164 1134 Planarity : 0.004 0.038 1134 Dihedral : 7.676 54.871 1460 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.71 % Allowed : 15.72 % Favored : 81.57 % 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: 4.15 (0.30), residues: 822 helix: 3.57 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -2.81 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 280 HIS 0.004 0.001 HIS A 170 PHE 0.017 0.002 PHE A 525 TYR 0.009 0.001 TYR B 364 ARG 0.004 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.811 Fit side-chains REVERT: A 341 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7746 (ttp) REVERT: B 341 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7748 (ttp) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.2770 time to fit residues: 166.8298 Evaluate side-chains 116 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 174 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7152 Z= 0.216 Angle : 0.562 9.767 9740 Z= 0.281 Chirality : 0.038 0.169 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.681 55.108 1460 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.71 % Allowed : 16.26 % Favored : 81.03 % 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: 4.06 (0.30), residues: 822 helix: 3.52 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -2.95 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 280 HIS 0.003 0.001 HIS B 170 PHE 0.017 0.002 PHE A 525 TYR 0.011 0.001 TYR A 571 ARG 0.003 0.000 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.841 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 1.1422 time to fit residues: 135.4690 Evaluate side-chains 116 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN B 174 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7152 Z= 0.205 Angle : 0.553 9.177 9740 Z= 0.277 Chirality : 0.038 0.169 1134 Planarity : 0.004 0.038 1134 Dihedral : 7.660 56.039 1460 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 16.80 % Favored : 81.30 % 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: 4.04 (0.30), residues: 822 helix: 3.53 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.97 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 280 HIS 0.003 0.001 HIS A 170 PHE 0.017 0.002 PHE A 525 TYR 0.009 0.001 TYR A 364 ARG 0.003 0.000 ARG A 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.780 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 1.1983 time to fit residues: 136.4819 Evaluate side-chains 112 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.0050 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.168984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118708 restraints weight = 7158.685| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.27 r_work: 0.3213 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7152 Z= 0.154 Angle : 0.530 8.684 9740 Z= 0.265 Chirality : 0.037 0.169 1134 Planarity : 0.004 0.042 1134 Dihedral : 7.551 57.492 1460 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.44 % Allowed : 16.80 % Favored : 80.76 % 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: 4.18 (0.30), residues: 822 helix: 3.62 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.95 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS B 176 PHE 0.015 0.001 PHE B 525 TYR 0.008 0.001 TYR A 571 ARG 0.003 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.23 seconds wall clock time: 51 minutes 13.17 seconds (3073.17 seconds total)