Starting phenix.real_space_refine on Mon Apr 28 07:27:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_9360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_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/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_9360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_9360.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_9360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf4_9360/04_2025/6nf4_9360.cif" } 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. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.13, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 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: 0.51 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: 2.05 Time building geometry restraints manager: 2.25 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: 0.00 - 1.85: 9028 1.85 - 3.71: 552 3.71 - 5.56: 108 5.56 - 7.41: 44 7.41 - 9.26: 8 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 3.040 nonbonded pdb=" O ARG A 379 " pdb=" OG1 THR A 383 " model vdw 2.379 3.040 nonbonded pdb=" OG1 THR B 216 " pdb=" ND2 ASN B 562 " model vdw 2.393 3.120 nonbonded pdb=" OG1 THR A 216 " pdb=" ND2 ASN A 562 " model vdw 2.393 3.120 nonbonded pdb=" O GLN A 515 " pdb=" ND2 ASN A 519 " model vdw 2.408 3.120 ... (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 Time spend for trying shortcut: 0.04 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: 18.920 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:81.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.960 ------------------------------------------------------------------------------- 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= 0.391 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 Details of bonding type rmsd hydrogen bonds : bond 0.11727 ( 568) hydrogen bonds : angle 5.08809 ( 1692) covalent geometry : bond 0.00901 ( 7152) covalent geometry : angle 1.09187 ( 9740) *********************** 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 to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.798 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: 1.9235 time to fit residues: 297.2669 Evaluate side-chains 100 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 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 433 GLN A 562 ASN B 433 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116170 restraints weight = 7126.139| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.25 r_work: 0.3183 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1705 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= 0.136 Angle : 0.554 6.696 9740 Z= 0.288 Chirality : 0.039 0.150 1134 Planarity : 0.004 0.034 1134 Dihedral : 9.714 55.235 1460 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.98 % Allowed : 9.49 % Favored : 87.53 % 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: 2.71 (0.29), residues: 822 helix: 2.50 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -2.60 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 417 HIS 0.002 0.001 HIS B 167 PHE 0.015 0.002 PHE B 525 TYR 0.010 0.001 TYR B 189 ARG 0.005 0.001 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 568) hydrogen bonds : angle 3.53310 ( 1692) covalent geometry : bond 0.00281 ( 7152) covalent geometry : angle 0.55428 ( 9740) *********************** 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 136 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.943 Fit side-chains REVERT: A 84 GLU cc_start: 0.8183 (pm20) cc_final: 0.7836 (mp0) REVERT: A 179 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7980 (m100) REVERT: A 275 MET cc_start: 0.8368 (mtp) cc_final: 0.8070 (mtm) REVERT: A 364 TYR cc_start: 0.9014 (m-10) cc_final: 0.8690 (m-80) REVERT: A 443 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7852 (mtm180) REVERT: B 84 GLU cc_start: 0.8200 (pm20) cc_final: 0.7850 (mp0) REVERT: B 179 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.7984 (m100) REVERT: B 275 MET cc_start: 0.8369 (mtp) cc_final: 0.8071 (mtm) REVERT: B 364 TYR cc_start: 0.9009 (m-10) cc_final: 0.8687 (m-80) REVERT: B 443 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7849 (mtm180) outliers start: 22 outliers final: 4 residues processed: 130 average time/residue: 1.4383 time to fit residues: 196.2094 Evaluate side-chains 114 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 179 TRP 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 20 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120334 restraints weight = 7260.495| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.28 r_work: 0.2996 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7152 Z= 0.120 Angle : 0.515 7.833 9740 Z= 0.265 Chirality : 0.037 0.140 1134 Planarity : 0.004 0.036 1134 Dihedral : 9.033 55.135 1460 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.52 % Allowed : 11.11 % 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: 3.52 (0.30), residues: 822 helix: 3.03 (0.18), residues: 710 sheet: None (None), residues: 0 loop : -2.83 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 280 HIS 0.002 0.001 HIS A 327 PHE 0.015 0.001 PHE B 202 TYR 0.012 0.001 TYR A 442 ARG 0.004 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 568) hydrogen bonds : angle 3.27250 ( 1692) covalent geometry : bond 0.00246 ( 7152) covalent geometry : angle 0.51540 ( 9740) *********************** 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 144 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.694 Fit side-chains REVERT: A 84 GLU cc_start: 0.7964 (pm20) cc_final: 0.7741 (mp0) REVERT: A 128 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6852 (mtt-85) REVERT: A 179 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7961 (t60) REVERT: A 275 MET cc_start: 0.8292 (mtp) cc_final: 0.7978 (mtm) REVERT: A 364 TYR cc_start: 0.8902 (m-10) cc_final: 0.8582 (m-80) REVERT: A 391 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 443 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7595 (mtm180) REVERT: B 84 GLU cc_start: 0.7967 (pm20) cc_final: 0.7743 (mp0) REVERT: B 128 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6854 (mtt-85) REVERT: B 179 TRP cc_start: 0.8284 (OUTLIER) cc_final: 0.7963 (t60) REVERT: B 275 MET cc_start: 0.8282 (mtp) cc_final: 0.7968 (mtm) REVERT: B 364 TYR cc_start: 0.8901 (m-10) cc_final: 0.8581 (m-80) REVERT: B 391 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8240 (mp) REVERT: B 443 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7590 (mtm180) outliers start: 26 outliers final: 6 residues processed: 128 average time/residue: 1.3483 time to fit residues: 181.0822 Evaluate side-chains 116 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 253 MET 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 179 TRP Chi-restraints excluded: chain B residue 253 MET 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 69 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 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 176 HIS A 433 GLN B 176 HIS B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.166390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115694 restraints weight = 7349.587| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.30 r_work: 0.3189 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7152 Z= 0.127 Angle : 0.518 9.188 9740 Z= 0.259 Chirality : 0.037 0.149 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.601 59.717 1460 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.25 % Allowed : 13.01 % Favored : 83.74 % 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: 3.87 (0.30), residues: 822 helix: 3.28 (0.18), residues: 710 sheet: None (None), residues: 0 loop : -2.84 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 280 HIS 0.004 0.001 HIS B 327 PHE 0.016 0.001 PHE A 202 TYR 0.008 0.001 TYR A 189 ARG 0.004 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 568) hydrogen bonds : angle 3.17142 ( 1692) covalent geometry : bond 0.00279 ( 7152) covalent geometry : angle 0.51769 ( 9740) *********************** 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 to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.732 Fit side-chains REVERT: A 128 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7101 (mtt-85) REVERT: A 179 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.8072 (t60) REVERT: A 267 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: A 336 GLU cc_start: 0.6151 (pm20) cc_final: 0.5734 (mm-30) REVERT: A 364 TYR cc_start: 0.8952 (m-10) cc_final: 0.8574 (m-80) REVERT: A 391 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 443 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7800 (mtm180) REVERT: B 128 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7109 (mtt-85) REVERT: B 179 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.8076 (t60) REVERT: B 267 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: B 334 MET cc_start: 0.7240 (mtp) cc_final: 0.7036 (mtp) REVERT: B 336 GLU cc_start: 0.6143 (pm20) cc_final: 0.5730 (mm-30) REVERT: B 364 TYR cc_start: 0.8949 (m-10) cc_final: 0.8569 (m-80) REVERT: B 391 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 443 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7800 (mtm180) outliers start: 24 outliers final: 8 residues processed: 122 average time/residue: 1.3389 time to fit residues: 171.2243 Evaluate side-chains 122 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP 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 433 GLN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP 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 433 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 A 433 GLN B 174 GLN B 410 GLN B 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116624 restraints weight = 7273.898| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.27 r_work: 0.3195 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7152 Z= 0.123 Angle : 0.516 8.839 9740 Z= 0.258 Chirality : 0.037 0.157 1134 Planarity : 0.003 0.037 1134 Dihedral : 8.388 56.030 1460 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.71 % Allowed : 13.55 % Favored : 83.74 % 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: 4.05 (0.30), residues: 822 helix: 3.45 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.97 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 179 HIS 0.002 0.001 HIS A 170 PHE 0.015 0.001 PHE B 202 TYR 0.012 0.001 TYR A 442 ARG 0.003 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 568) hydrogen bonds : angle 3.11023 ( 1692) covalent geometry : bond 0.00264 ( 7152) covalent geometry : angle 0.51638 ( 9740) *********************** 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 132 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.608 Fit side-chains REVERT: A 128 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7051 (mtt-85) REVERT: A 179 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.8062 (t60) REVERT: A 267 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: A 336 GLU cc_start: 0.6150 (pm20) cc_final: 0.5721 (mm-30) REVERT: A 364 TYR cc_start: 0.8935 (m-10) cc_final: 0.8576 (m-80) REVERT: A 391 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 443 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7818 (mtm180) REVERT: B 128 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7049 (mtt-85) REVERT: B 179 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.8069 (t60) REVERT: B 267 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: B 336 GLU cc_start: 0.6140 (pm20) cc_final: 0.5712 (mm-30) REVERT: B 364 TYR cc_start: 0.8935 (m-10) cc_final: 0.8575 (m-80) REVERT: B 391 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8387 (mp) REVERT: B 443 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7813 (mtm180) outliers start: 20 outliers final: 6 residues processed: 124 average time/residue: 1.3106 time to fit residues: 170.5937 Evaluate side-chains 122 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP 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 B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN A 519 ASN B 174 GLN B 433 GLN B 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.169128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118113 restraints weight = 7288.314| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.30 r_work: 0.3183 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2445 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= 0.130 Angle : 0.513 8.983 9740 Z= 0.256 Chirality : 0.037 0.164 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.089 53.618 1460 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.44 % Allowed : 15.18 % Favored : 82.38 % 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: 4.07 (0.30), residues: 822 helix: 3.45 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -2.92 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 280 HIS 0.002 0.001 HIS B 170 PHE 0.017 0.001 PHE B 525 TYR 0.008 0.001 TYR A 189 ARG 0.008 0.001 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 568) hydrogen bonds : angle 3.03983 ( 1692) covalent geometry : bond 0.00289 ( 7152) covalent geometry : angle 0.51274 ( 9740) *********************** 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 134 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.729 Fit side-chains REVERT: A 84 GLU cc_start: 0.8212 (mp0) cc_final: 0.7933 (mp0) REVERT: A 179 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.8017 (t60) REVERT: A 267 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: A 336 GLU cc_start: 0.6227 (pm20) cc_final: 0.5909 (mm-30) REVERT: A 364 TYR cc_start: 0.8953 (m-10) cc_final: 0.8720 (m-80) REVERT: A 443 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7854 (mtm180) REVERT: B 84 GLU cc_start: 0.8219 (mp0) cc_final: 0.7944 (mp0) REVERT: B 179 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (t60) REVERT: B 267 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: B 336 GLU cc_start: 0.6215 (pm20) cc_final: 0.5915 (mm-30) REVERT: B 364 TYR cc_start: 0.8954 (m-10) cc_final: 0.8722 (m-80) REVERT: B 443 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7849 (mtm180) outliers start: 18 outliers final: 6 residues processed: 128 average time/residue: 1.3140 time to fit residues: 176.4789 Evaluate side-chains 124 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.169258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118534 restraints weight = 7144.173| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.27 r_work: 0.3189 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2446 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= 0.124 Angle : 0.508 9.016 9740 Z= 0.253 Chirality : 0.037 0.167 1134 Planarity : 0.004 0.040 1134 Dihedral : 7.973 54.099 1460 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.52 % Allowed : 13.82 % Favored : 82.66 % 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: 4.12 (0.30), residues: 822 helix: 3.50 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.97 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.003 0.001 HIS B 170 PHE 0.016 0.001 PHE A 525 TYR 0.012 0.001 TYR A 442 ARG 0.006 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 568) hydrogen bonds : angle 3.01248 ( 1692) covalent geometry : bond 0.00271 ( 7152) covalent geometry : angle 0.50776 ( 9740) *********************** 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 138 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.737 Fit side-chains REVERT: A 84 GLU cc_start: 0.8215 (mp0) cc_final: 0.7936 (mp0) REVERT: A 179 TRP cc_start: 0.8273 (OUTLIER) cc_final: 0.8047 (t60) REVERT: A 267 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: A 336 GLU cc_start: 0.6123 (pm20) cc_final: 0.5775 (mm-30) REVERT: A 364 TYR cc_start: 0.8949 (m-10) cc_final: 0.8722 (m-80) REVERT: A 391 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 443 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7853 (mtm180) REVERT: B 84 GLU cc_start: 0.8221 (mp0) cc_final: 0.7941 (mp0) REVERT: B 179 TRP cc_start: 0.8273 (OUTLIER) cc_final: 0.8044 (t60) REVERT: B 267 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: B 336 GLU cc_start: 0.6115 (pm20) cc_final: 0.5777 (mm-30) REVERT: B 364 TYR cc_start: 0.8952 (m-10) cc_final: 0.8725 (m-80) REVERT: B 391 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 443 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7851 (mtm180) outliers start: 26 outliers final: 8 residues processed: 126 average time/residue: 1.1859 time to fit residues: 157.2495 Evaluate side-chains 124 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 341 MET 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 179 TRP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 341 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN A 562 ASN B 433 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.170947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119921 restraints weight = 7218.414| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.34 r_work: 0.3209 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7152 Z= 0.112 Angle : 0.494 8.281 9740 Z= 0.246 Chirality : 0.036 0.168 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.614 56.139 1460 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.71 % Allowed : 14.63 % Favored : 82.66 % 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: 4.31 (0.30), residues: 822 helix: 3.69 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.75 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 179 HIS 0.002 0.000 HIS A 176 PHE 0.015 0.001 PHE A 525 TYR 0.008 0.001 TYR A 442 ARG 0.006 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 568) hydrogen bonds : angle 2.93399 ( 1692) covalent geometry : bond 0.00238 ( 7152) covalent geometry : angle 0.49393 ( 9740) *********************** 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 134 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.739 Fit side-chains REVERT: A 84 GLU cc_start: 0.8194 (mp0) cc_final: 0.7929 (mp0) REVERT: A 179 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7995 (t60) REVERT: A 336 GLU cc_start: 0.6068 (pm20) cc_final: 0.5724 (mm-30) REVERT: A 364 TYR cc_start: 0.8938 (m-10) cc_final: 0.8637 (m-80) REVERT: A 391 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 443 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7785 (mtm180) REVERT: B 84 GLU cc_start: 0.8213 (mp0) cc_final: 0.7949 (mp0) REVERT: B 179 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.7992 (t60) REVERT: B 336 GLU cc_start: 0.6053 (pm20) cc_final: 0.5719 (mm-30) REVERT: B 364 TYR cc_start: 0.8937 (m-10) cc_final: 0.8638 (m-80) REVERT: B 391 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 443 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7780 (mtm180) outliers start: 20 outliers final: 4 residues processed: 120 average time/residue: 1.2991 time to fit residues: 163.8443 Evaluate side-chains 124 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP 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 179 TRP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 57 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 A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.170561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119967 restraints weight = 7329.427| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.27 r_work: 0.3207 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7152 Z= 0.120 Angle : 0.499 8.457 9740 Z= 0.248 Chirality : 0.037 0.167 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.546 56.666 1460 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.90 % Allowed : 16.26 % Favored : 81.84 % 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: 4.32 (0.30), residues: 822 helix: 3.70 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.76 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS B 170 PHE 0.015 0.001 PHE B 202 TYR 0.012 0.001 TYR B 442 ARG 0.005 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 568) hydrogen bonds : angle 2.95072 ( 1692) covalent geometry : bond 0.00259 ( 7152) covalent geometry : angle 0.49890 ( 9740) *********************** 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 128 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.675 Fit side-chains REVERT: A 84 GLU cc_start: 0.8207 (mp0) cc_final: 0.7949 (mp0) REVERT: A 179 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (t60) REVERT: A 336 GLU cc_start: 0.6073 (pm20) cc_final: 0.5767 (mm-30) REVERT: A 364 TYR cc_start: 0.8951 (m-10) cc_final: 0.8733 (m-80) REVERT: A 391 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 443 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7809 (mtm180) REVERT: B 84 GLU cc_start: 0.8223 (mp0) cc_final: 0.7966 (mp0) REVERT: B 179 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7983 (t60) REVERT: B 336 GLU cc_start: 0.6055 (pm20) cc_final: 0.5757 (mm-30) REVERT: B 364 TYR cc_start: 0.8948 (m-10) cc_final: 0.8734 (m-80) REVERT: B 391 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 443 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7801 (mtm180) outliers start: 14 outliers final: 4 residues processed: 124 average time/residue: 1.4597 time to fit residues: 189.3286 Evaluate side-chains 120 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP 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 179 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118323 restraints weight = 7384.912| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.29 r_work: 0.3216 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7152 Z= 0.114 Angle : 0.497 8.321 9740 Z= 0.248 Chirality : 0.036 0.168 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.492 57.479 1460 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.90 % Allowed : 16.53 % 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: 4.26 (0.30), residues: 822 helix: 3.66 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.80 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.002 0.001 HIS A 176 PHE 0.015 0.001 PHE B 177 TYR 0.011 0.001 TYR B 344 ARG 0.004 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 568) hydrogen bonds : angle 2.94809 ( 1692) covalent geometry : bond 0.00241 ( 7152) covalent geometry : angle 0.49685 ( 9740) ********************** 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 126 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.899 Fit side-chains REVERT: A 84 GLU cc_start: 0.8197 (mp0) cc_final: 0.7948 (mp0) REVERT: A 179 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (t60) REVERT: A 336 GLU cc_start: 0.6106 (pm20) cc_final: 0.5802 (mm-30) REVERT: A 364 TYR cc_start: 0.8931 (m-10) cc_final: 0.8699 (m-80) REVERT: A 391 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 443 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7772 (mtm180) REVERT: B 84 GLU cc_start: 0.8210 (mp0) cc_final: 0.7962 (mp0) REVERT: B 179 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7911 (t60) REVERT: B 336 GLU cc_start: 0.6094 (pm20) cc_final: 0.5790 (mm-30) REVERT: B 364 TYR cc_start: 0.8934 (m-10) cc_final: 0.8706 (m-80) REVERT: B 391 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 443 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7763 (mtm180) outliers start: 14 outliers final: 6 residues processed: 122 average time/residue: 1.4704 time to fit residues: 189.0508 Evaluate side-chains 120 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP 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 530 SER Chi-restraints excluded: chain B residue 179 TRP 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 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 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 A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116659 restraints weight = 7344.970| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.32 r_work: 0.3199 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2731 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= 0.126 Angle : 0.509 8.744 9740 Z= 0.252 Chirality : 0.037 0.167 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.466 57.381 1460 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % 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: 4.22 (0.30), residues: 822 helix: 3.64 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.83 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS A 170 PHE 0.015 0.001 PHE B 525 TYR 0.013 0.001 TYR A 442 ARG 0.004 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 568) hydrogen bonds : angle 2.97011 ( 1692) covalent geometry : bond 0.00282 ( 7152) covalent geometry : angle 0.50888 ( 9740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5344.20 seconds wall clock time: 94 minutes 51.58 seconds (5691.58 seconds total)