Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 11:23:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/04_2023/6nf4_9360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/04_2023/6nf4_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_9360/04_2023/6nf4_9360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/04_2023/6nf4_9360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/04_2023/6nf4_9360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf4_9360/04_2023/6nf4_9360.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.41, 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: 3.01 Conformation dependent library (CDL) restraints added in 984.1 milliseconds 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: 0.19 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: 1.89 Time building geometry restraints manager: 3.21 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: 3792 17.88 - 35.75: 238 35.75 - 53.63: 48 53.63 - 71.51: 10 71.51 - 89.38: 10 Dihedral angle restraints: 4098 sinusoidal: 1642 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 4095 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: 0.570 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: 0.010 Extract box with map and model: 2.460 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.080 Find NCS groups from input model: 0.340 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- 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 : 13.645 89.384 2514 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 % 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 *********************** 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 : 0.708 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 1.4164 time to fit residues: 218.8429 Evaluate side-chains 100 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0602 ------------------------------------------------------------------------------- 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: 0.5980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.1717 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= 0.165 Angle : 0.543 6.307 9740 Z= 0.282 Chirality : 0.037 0.146 1134 Planarity : 0.004 0.033 1134 Dihedral : 9.557 56.774 1000 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 3.25 % 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: 2.77 (0.29), residues: 822 helix: 2.53 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -2.58 (0.56), residues: 124 *********************** 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 138 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.839 Fit side-chains outliers start: 24 outliers final: 6 residues processed: 132 average time/residue: 1.1674 time to fit residues: 162.7981 Evaluate side-chains 112 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1332 time to fit residues: 1.4771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0170 chunk 23 optimal weight: 0.0030 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4228 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 7152 Z= 0.143 Angle : 0.510 8.185 9740 Z= 0.261 Chirality : 0.036 0.138 1134 Planarity : 0.004 0.036 1134 Dihedral : 9.188 57.737 1000 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 4.34 % 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: 3.60 (0.30), residues: 822 helix: 3.11 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.83 (0.58), residues: 116 *********************** 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 148 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.784 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 126 average time/residue: 1.2965 time to fit residues: 171.6379 Evaluate side-chains 120 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.3446 time to fit residues: 4.2049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 176 HIS B 174 GLN B 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2206 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= 0.159 Angle : 0.516 9.018 9740 Z= 0.257 Chirality : 0.036 0.144 1134 Planarity : 0.004 0.037 1134 Dihedral : 8.946 57.099 1000 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 3.79 % 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: 3.93 (0.30), residues: 822 helix: 3.36 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.89 (0.56), residues: 116 *********************** 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: 28 poor density : 104 time to evaluate : 0.766 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 112 average time/residue: 1.2183 time to fit residues: 143.9601 Evaluate side-chains 118 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 8 average time/residue: 0.9027 time to fit residues: 8.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7152 Z= 0.177 Angle : 0.513 8.872 9740 Z= 0.256 Chirality : 0.037 0.152 1134 Planarity : 0.004 0.037 1134 Dihedral : 8.617 56.929 1000 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.30), residues: 822 helix: 3.41 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -2.81 (0.59), residues: 114 *********************** 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 126 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.795 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 110 average time/residue: 1.2393 time to fit residues: 143.5770 Evaluate side-chains 114 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 6 average time/residue: 0.5930 time to fit residues: 4.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 7152 Z= 0.227 Angle : 0.551 9.389 9740 Z= 0.275 Chirality : 0.038 0.164 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.459 56.217 1000 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 3.25 % 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: 3.90 (0.30), residues: 822 helix: 3.34 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -3.06 (0.56), residues: 114 *********************** 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 130 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.883 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 1.1976 time to fit residues: 151.8621 Evaluate side-chains 114 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.5919 time to fit residues: 3.7411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 32 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7152 Z= 0.142 Angle : 0.494 8.549 9740 Z= 0.246 Chirality : 0.036 0.166 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.198 57.640 1000 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.30), residues: 822 helix: 3.67 (0.18), residues: 694 sheet: None (None), residues: 0 loop : -2.88 (0.54), residues: 128 *********************** 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 136 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.787 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 1.2822 time to fit residues: 167.2655 Evaluate side-chains 118 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.6530 time to fit residues: 5.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.2614 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= 0.182 Angle : 0.529 8.879 9740 Z= 0.260 Chirality : 0.037 0.168 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.017 57.313 1000 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 2.71 % 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: 3.60 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.89 (0.54), residues: 126 *********************** 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 132 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.877 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.2702 time to fit residues: 165.6958 Evaluate side-chains 116 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1131 time to fit residues: 1.4344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7152 Z= 0.168 Angle : 0.546 9.927 9740 Z= 0.273 Chirality : 0.037 0.168 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.007 57.648 1000 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.90 % 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: 3.61 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.98 (0.55), residues: 126 *********************** 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 118 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.792 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 1.1494 time to fit residues: 136.3557 Evaluate side-chains 114 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.0953 time to fit residues: 1.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0000 chunk 55 optimal weight: 0.1980 chunk 83 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.2202 ------------------------------------------------------------------------------- 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** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7152 Z= 0.139 Angle : 0.530 8.949 9740 Z= 0.267 Chirality : 0.036 0.165 1134 Planarity : 0.004 0.038 1134 Dihedral : 7.888 58.617 1000 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.08 % 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: 4.27 (0.30), residues: 822 helix: 3.70 (0.18), residues: 694 sheet: None (None), residues: 0 loop : -2.85 (0.56), residues: 128 ********************** 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 122 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.775 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 1.1655 time to fit residues: 148.0173 Evaluate side-chains 108 residues out of total 738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118855 restraints weight = 7123.415| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.26 r_work: 0.3222 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7152 Z= 0.163 Angle : 0.541 9.216 9740 Z= 0.268 Chirality : 0.037 0.164 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.866 58.233 1000 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.08 % 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: 4.23 (0.30), residues: 822 helix: 3.65 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.88 (0.58), residues: 126 =============================================================================== Job complete usr+sys time: 2803.38 seconds wall clock time: 50 minutes 39.25 seconds (3039.25 seconds total)