Starting phenix.real_space_refine on Tue Feb 11 05:25:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.map" model { file = "/net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c02_16353/02_2025/8c02_16353.cif" } resolution = 4.09 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= 0.001 sd= 0.027 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 31 5.16 5 C 2767 2.51 5 N 695 2.21 5 O 749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4242 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 2.57, per 1000 atoms: 0.61 Number of scatterers: 4242 At special positions: 0 Unit cell: (76.818, 100.254, 72.912, 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 31 16.00 O 749 8.00 N 695 7.00 C 2767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 521.6 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 72.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.897A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 127 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.077A pdb=" N VAL A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.856A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.695A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 Processing helix chain 'A' and resid 451 through 483 removed outlier: 3.642A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 546 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS B 101 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR B 112 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 103 " --> pdb=" O TYR B 110 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1014 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: 1.29 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1312 1.34 - 1.46: 1032 1.46 - 1.58: 1939 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4335 Sorted by residual: bond pdb=" N MET A 288 " pdb=" CA MET A 288 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.25e-02 6.40e+03 8.87e+00 bond pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.32e-02 5.74e+03 5.40e+00 bond pdb=" CG GLN A 93 " pdb=" CD GLN A 93 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.31e+00 bond pdb=" CG1 ILE A 136 " pdb=" CD1 ILE A 136 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CG LEU A 222 " pdb=" CD1 LEU A 222 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 4330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5701 1.98 - 3.97: 149 3.97 - 5.95: 33 5.95 - 7.94: 12 7.94 - 9.92: 3 Bond angle restraints: 5898 Sorted by residual: angle pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLU A 486 " pdb=" CB GLU A 486 " pdb=" CG GLU A 486 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" N GLN A 93 " pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " ideal model delta sigma weight residual 110.28 115.21 -4.93 1.55e+00 4.16e-01 1.01e+01 angle pdb=" CB LYS A 549 " pdb=" CG LYS A 549 " pdb=" CD LYS A 549 " ideal model delta sigma weight residual 111.30 118.34 -7.04 2.30e+00 1.89e-01 9.36e+00 angle pdb=" CA GLU A 290 " pdb=" CB GLU A 290 " pdb=" CG GLU A 290 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.81e+00 ... (remaining 5893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 2262 16.19 - 32.38: 187 32.38 - 48.57: 43 48.57 - 64.76: 7 64.76 - 80.95: 5 Dihedral angle restraints: 2504 sinusoidal: 930 harmonic: 1574 Sorted by residual: dihedral pdb=" CA THR A 122 " pdb=" C THR A 122 " pdb=" N MET A 123 " pdb=" CA MET A 123 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU B 46 " pdb=" C GLU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA MET B 105 " pdb=" C MET B 105 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 473 0.039 - 0.077: 164 0.077 - 0.116: 48 0.116 - 0.155: 7 0.155 - 0.193: 4 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLN A 93 " pdb=" N GLN A 93 " pdb=" C GLN A 93 " pdb=" CB GLN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE B 56 " pdb=" CA ILE B 56 " pdb=" CG1 ILE B 56 " pdb=" CG2 ILE B 56 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 693 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 514 " -0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 515 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 29 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO B 30 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 317 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C LEU A 317 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 317 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 318 " -0.015 2.00e-02 2.50e+03 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 718 2.76 - 3.29: 4563 3.29 - 3.83: 7381 3.83 - 4.36: 7786 4.36 - 4.90: 13676 Nonbonded interactions: 34124 Sorted by model distance: nonbonded pdb=" O CYS B 24 " pdb=" OG1 THR B 80 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 358 " pdb=" OG1 THR A 361 " model vdw 2.279 3.040 nonbonded pdb=" O ALA B 54 " pdb=" NH2 ARG B 74 " model vdw 2.298 3.120 nonbonded pdb=" N MET B 105 " pdb=" O TRP B 108 " model vdw 2.323 3.120 nonbonded pdb=" O THR A 230 " pdb=" OG1 THR A 230 " model vdw 2.339 3.040 ... (remaining 34119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.004 0.057 4335 Z= 0.259 Angle : 0.832 9.920 5898 Z= 0.419 Chirality : 0.045 0.193 696 Planarity : 0.007 0.083 719 Dihedral : 13.159 80.949 1497 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.44 % Allowed : 0.00 % Favored : 99.56 % 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: 1.51 (0.35), residues: 541 helix: 2.10 (0.26), residues: 367 sheet: -1.31 (0.64), residues: 39 loop : -1.40 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 38 HIS 0.002 0.001 HIS A 32 PHE 0.016 0.002 PHE A 530 TYR 0.030 0.002 TYR A 29 ARG 0.007 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80) REVERT: A 36 THR cc_start: 0.9349 (m) cc_final: 0.9145 (t) REVERT: A 111 MET cc_start: 0.8545 (tpt) cc_final: 0.8277 (mmm) REVERT: A 184 THR cc_start: 0.9334 (m) cc_final: 0.8956 (t) REVERT: A 290 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20) REVERT: A 312 MET cc_start: 0.8837 (tpt) cc_final: 0.8058 (tpp) REVERT: A 473 ASP cc_start: 0.9390 (t70) cc_final: 0.9177 (t0) REVERT: A 536 ILE cc_start: 0.8342 (mm) cc_final: 0.8104 (mm) REVERT: B 20 LEU cc_start: 0.8822 (tt) cc_final: 0.8434 (mt) REVERT: B 70 PHE cc_start: 0.7802 (m-10) cc_final: 0.7413 (m-80) REVERT: B 92 ASP cc_start: 0.7493 (m-30) cc_final: 0.6904 (m-30) REVERT: B 119 VAL cc_start: 0.9269 (t) cc_final: 0.9062 (t) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1340 time to fit residues: 32.9374 Evaluate side-chains 159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 335 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109731 restraints weight = 8695.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113197 restraints weight = 5007.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115611 restraints weight = 3440.085| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4335 Z= 0.197 Angle : 0.654 8.460 5898 Z= 0.333 Chirality : 0.040 0.164 696 Planarity : 0.005 0.065 719 Dihedral : 4.110 15.643 590 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: 2.05 (0.36), residues: 541 helix: 2.44 (0.26), residues: 369 sheet: -0.11 (0.73), residues: 43 loop : -1.41 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 38 HIS 0.003 0.001 HIS A 32 PHE 0.007 0.001 PHE A 295 TYR 0.024 0.002 TYR A 29 ARG 0.005 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8564 (tpt) cc_final: 0.8174 (mmm) REVERT: A 179 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: A 180 ILE cc_start: 0.8283 (mm) cc_final: 0.8064 (mm) REVERT: A 290 GLU cc_start: 0.8599 (pm20) cc_final: 0.8397 (pm20) REVERT: A 488 GLU cc_start: 0.7353 (tp30) cc_final: 0.7070 (tp30) REVERT: A 536 ILE cc_start: 0.8265 (mm) cc_final: 0.8048 (mm) REVERT: B 6 LEU cc_start: 0.8595 (pp) cc_final: 0.8264 (pp) REVERT: B 8 GLU cc_start: 0.7528 (mp0) cc_final: 0.5840 (mp0) REVERT: B 34 ASN cc_start: 0.8100 (m-40) cc_final: 0.7608 (m110) REVERT: B 38 TRP cc_start: 0.8297 (m100) cc_final: 0.7987 (m100) REVERT: B 70 PHE cc_start: 0.7751 (m-10) cc_final: 0.7416 (m-80) REVERT: B 85 MET cc_start: 0.7838 (mmp) cc_final: 0.7637 (mmp) REVERT: B 92 ASP cc_start: 0.7332 (m-30) cc_final: 0.6863 (m-30) REVERT: B 108 TRP cc_start: 0.8136 (t-100) cc_final: 0.7339 (t-100) REVERT: B 117 THR cc_start: 0.8809 (p) cc_final: 0.8551 (t) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1581 time to fit residues: 39.9196 Evaluate side-chains 168 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.137117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109162 restraints weight = 8603.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112736 restraints weight = 4846.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115175 restraints weight = 3252.442| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4335 Z= 0.213 Angle : 0.633 8.883 5898 Z= 0.326 Chirality : 0.040 0.169 696 Planarity : 0.004 0.045 719 Dihedral : 3.954 16.994 590 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.22 % Allowed : 3.08 % Favored : 96.70 % 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: 1.96 (0.36), residues: 541 helix: 2.35 (0.26), residues: 371 sheet: -0.17 (0.83), residues: 38 loop : -1.43 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.009 0.001 PHE A 292 TYR 0.018 0.002 TYR B 62 ARG 0.007 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8813 (t80) cc_final: 0.8542 (t80) REVERT: A 29 TYR cc_start: 0.9286 (m-10) cc_final: 0.9035 (m-10) REVERT: A 79 ILE cc_start: 0.9001 (mm) cc_final: 0.8784 (tp) REVERT: A 179 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8087 (ttm110) REVERT: A 180 ILE cc_start: 0.8316 (mm) cc_final: 0.8085 (mm) REVERT: A 312 MET cc_start: 0.8546 (tpp) cc_final: 0.7376 (tpp) REVERT: A 536 ILE cc_start: 0.8244 (mm) cc_final: 0.8032 (mm) REVERT: B 34 ASN cc_start: 0.8165 (m-40) cc_final: 0.7685 (m110) REVERT: B 36 MET cc_start: 0.8978 (mmm) cc_final: 0.8761 (mmm) REVERT: B 38 TRP cc_start: 0.8177 (m100) cc_final: 0.7897 (m100) REVERT: B 92 ASP cc_start: 0.7270 (m-30) cc_final: 0.6741 (m-30) REVERT: B 108 TRP cc_start: 0.8373 (t-100) cc_final: 0.7810 (t-100) REVERT: B 119 VAL cc_start: 0.8866 (m) cc_final: 0.8554 (m) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1448 time to fit residues: 34.6091 Evaluate side-chains 159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108806 restraints weight = 8739.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112395 restraints weight = 4893.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114892 restraints weight = 3258.031| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4335 Z= 0.218 Angle : 0.648 8.584 5898 Z= 0.331 Chirality : 0.040 0.145 696 Planarity : 0.004 0.069 719 Dihedral : 3.945 15.544 590 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.44 % Allowed : 4.19 % Favored : 95.37 % 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: 2.14 (0.37), residues: 541 helix: 2.43 (0.26), residues: 372 sheet: 0.15 (0.89), residues: 38 loop : -1.25 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.012 0.001 PHE A 530 TYR 0.020 0.001 TYR A 302 ARG 0.004 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8758 (t80) cc_final: 0.8450 (t80) REVERT: A 111 MET cc_start: 0.8269 (mmm) cc_final: 0.7931 (mmm) REVERT: A 119 GLU cc_start: 0.8062 (pm20) cc_final: 0.7787 (pm20) REVERT: A 180 ILE cc_start: 0.8335 (mm) cc_final: 0.8116 (mm) REVERT: A 293 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8442 (ptp-110) REVERT: A 302 TYR cc_start: 0.8569 (t80) cc_final: 0.8076 (t80) REVERT: A 309 LEU cc_start: 0.8766 (mt) cc_final: 0.8350 (mt) REVERT: A 335 GLN cc_start: 0.7469 (tp40) cc_final: 0.6626 (tt0) REVERT: A 485 ILE cc_start: 0.8875 (mp) cc_final: 0.8346 (mt) REVERT: B 34 ASN cc_start: 0.8129 (m-40) cc_final: 0.7692 (m-40) REVERT: B 36 MET cc_start: 0.8982 (mmm) cc_final: 0.8749 (mmm) REVERT: B 46 GLU cc_start: 0.7339 (pp20) cc_final: 0.7088 (pp20) REVERT: B 84 GLN cc_start: 0.8181 (tp40) cc_final: 0.7885 (tp40) REVERT: B 108 TRP cc_start: 0.8446 (t-100) cc_final: 0.8057 (t-100) REVERT: B 119 VAL cc_start: 0.8854 (m) cc_final: 0.8453 (m) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1500 time to fit residues: 35.7231 Evaluate side-chains 161 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.135877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108846 restraints weight = 8737.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112325 restraints weight = 4898.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114630 restraints weight = 3267.047| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4335 Z= 0.225 Angle : 0.676 8.767 5898 Z= 0.343 Chirality : 0.040 0.167 696 Planarity : 0.004 0.038 719 Dihedral : 3.941 15.709 590 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 3.08 % Favored : 96.70 % 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: 2.12 (0.37), residues: 541 helix: 2.39 (0.26), residues: 370 sheet: 0.21 (0.86), residues: 38 loop : -1.16 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 32 PHE 0.011 0.001 PHE B 70 TYR 0.015 0.001 TYR B 62 ARG 0.004 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8737 (t80) cc_final: 0.8401 (t80) REVERT: A 29 TYR cc_start: 0.9182 (m-10) cc_final: 0.8777 (m-80) REVERT: A 111 MET cc_start: 0.8258 (mmm) cc_final: 0.7857 (mmm) REVERT: A 119 GLU cc_start: 0.8096 (pm20) cc_final: 0.7867 (pm20) REVERT: A 180 ILE cc_start: 0.8210 (mm) cc_final: 0.7956 (mm) REVERT: A 335 GLN cc_start: 0.7546 (tp40) cc_final: 0.6444 (tt0) REVERT: B 21 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: B 22 LEU cc_start: 0.8843 (mm) cc_final: 0.8609 (mm) REVERT: B 34 ASN cc_start: 0.8339 (m-40) cc_final: 0.7910 (m110) REVERT: B 36 MET cc_start: 0.8993 (mmm) cc_final: 0.8741 (mmm) REVERT: B 72 ILE cc_start: 0.8243 (tp) cc_final: 0.8013 (tp) REVERT: B 80 THR cc_start: 0.8040 (t) cc_final: 0.7511 (t) REVERT: B 92 ASP cc_start: 0.7363 (m-30) cc_final: 0.6867 (m-30) REVERT: B 119 VAL cc_start: 0.8861 (m) cc_final: 0.8443 (m) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1380 time to fit residues: 33.4155 Evaluate side-chains 166 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 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 141 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108410 restraints weight = 8611.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111633 restraints weight = 5071.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113887 restraints weight = 3496.242| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4335 Z= 0.241 Angle : 0.683 8.820 5898 Z= 0.351 Chirality : 0.040 0.148 696 Planarity : 0.004 0.038 719 Dihedral : 3.917 15.286 590 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 2.06 (0.36), residues: 541 helix: 2.34 (0.26), residues: 370 sheet: 0.30 (0.84), residues: 38 loop : -1.19 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.004 0.001 HIS A 32 PHE 0.011 0.001 PHE A 292 TYR 0.015 0.001 TYR A 318 ARG 0.003 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8699 (t80) cc_final: 0.8392 (t80) REVERT: A 29 TYR cc_start: 0.9223 (m-10) cc_final: 0.8889 (m-80) REVERT: A 111 MET cc_start: 0.8315 (mmm) cc_final: 0.7954 (mmm) REVERT: A 119 GLU cc_start: 0.8084 (pm20) cc_final: 0.7787 (pm20) REVERT: A 180 ILE cc_start: 0.8213 (mm) cc_final: 0.7930 (mm) REVERT: A 335 GLN cc_start: 0.7711 (tp40) cc_final: 0.6790 (tt0) REVERT: B 30 PRO cc_start: 0.9478 (Cg_exo) cc_final: 0.8916 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8452 (m-40) cc_final: 0.8114 (m110) REVERT: B 36 MET cc_start: 0.9029 (mmm) cc_final: 0.8761 (mmm) REVERT: B 72 ILE cc_start: 0.8300 (tp) cc_final: 0.8067 (tp) REVERT: B 92 ASP cc_start: 0.7409 (m-30) cc_final: 0.7201 (m-30) REVERT: B 119 VAL cc_start: 0.8856 (m) cc_final: 0.8451 (m) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1400 time to fit residues: 33.6481 Evaluate side-chains 162 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.136388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109349 restraints weight = 9062.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112909 restraints weight = 5179.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115385 restraints weight = 3498.322| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4335 Z= 0.220 Angle : 0.673 8.798 5898 Z= 0.346 Chirality : 0.040 0.157 696 Planarity : 0.004 0.040 719 Dihedral : 3.904 14.827 590 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 1.99 (0.36), residues: 541 helix: 2.30 (0.26), residues: 369 sheet: -0.01 (0.76), residues: 43 loop : -1.15 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.004 0.001 HIS A 32 PHE 0.015 0.001 PHE A 292 TYR 0.018 0.001 TYR A 318 ARG 0.003 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8588 (t80) cc_final: 0.8383 (t80) REVERT: A 29 TYR cc_start: 0.9188 (m-10) cc_final: 0.8929 (m-80) REVERT: A 111 MET cc_start: 0.8298 (mmm) cc_final: 0.7886 (mmm) REVERT: A 119 GLU cc_start: 0.8341 (pm20) cc_final: 0.8023 (pm20) REVERT: A 335 GLN cc_start: 0.7666 (tp40) cc_final: 0.6676 (tt0) REVERT: B 30 PRO cc_start: 0.9354 (Cg_exo) cc_final: 0.8885 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8383 (m-40) cc_final: 0.7920 (m110) REVERT: B 36 MET cc_start: 0.9050 (mmm) cc_final: 0.8793 (mmm) REVERT: B 72 ILE cc_start: 0.8278 (tp) cc_final: 0.8012 (tp) REVERT: B 119 VAL cc_start: 0.8760 (m) cc_final: 0.8418 (m) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1428 time to fit residues: 33.6496 Evaluate side-chains 168 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** 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 = 0.3771 r_free = 0.3771 target = 0.136707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110392 restraints weight = 8309.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113591 restraints weight = 4906.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115898 restraints weight = 3357.394| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4335 Z= 0.237 Angle : 0.702 8.953 5898 Z= 0.361 Chirality : 0.040 0.169 696 Planarity : 0.004 0.042 719 Dihedral : 3.939 15.499 590 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 1.97 (0.37), residues: 541 helix: 2.27 (0.26), residues: 370 sheet: -0.03 (0.77), residues: 43 loop : -1.14 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 33 HIS 0.004 0.001 HIS A 32 PHE 0.017 0.001 PHE A 292 TYR 0.017 0.001 TYR A 318 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8596 (t80) cc_final: 0.8369 (t80) REVERT: A 29 TYR cc_start: 0.9181 (m-10) cc_final: 0.8901 (m-80) REVERT: A 30 LEU cc_start: 0.9422 (tp) cc_final: 0.9125 (tt) REVERT: A 111 MET cc_start: 0.8271 (mmm) cc_final: 0.7871 (mmm) REVERT: A 119 GLU cc_start: 0.8330 (pm20) cc_final: 0.8062 (pm20) REVERT: A 190 MET cc_start: 0.8485 (tmm) cc_final: 0.8265 (tmm) REVERT: A 335 GLN cc_start: 0.7625 (tp40) cc_final: 0.6672 (tt0) REVERT: B 30 PRO cc_start: 0.9356 (Cg_exo) cc_final: 0.8831 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8407 (m-40) cc_final: 0.7931 (m110) REVERT: B 36 MET cc_start: 0.9120 (mmm) cc_final: 0.8844 (mmm) REVERT: B 72 ILE cc_start: 0.8244 (tp) cc_final: 0.7980 (tp) REVERT: B 119 VAL cc_start: 0.8794 (m) cc_final: 0.8433 (m) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1358 time to fit residues: 31.8607 Evaluate side-chains 161 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** 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 = 0.3773 r_free = 0.3773 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109370 restraints weight = 8533.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112845 restraints weight = 4859.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115356 restraints weight = 3291.578| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4335 Z= 0.229 Angle : 0.728 9.520 5898 Z= 0.370 Chirality : 0.040 0.176 696 Planarity : 0.004 0.042 719 Dihedral : 3.960 15.145 590 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 1.97 (0.37), residues: 541 helix: 2.28 (0.26), residues: 370 sheet: -0.07 (0.74), residues: 43 loop : -1.17 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE A 541 TYR 0.016 0.001 TYR A 318 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8580 (t80) cc_final: 0.8339 (t80) REVERT: A 30 LEU cc_start: 0.9402 (tp) cc_final: 0.9113 (tt) REVERT: A 111 MET cc_start: 0.8280 (mmm) cc_final: 0.7865 (mmm) REVERT: A 119 GLU cc_start: 0.8362 (pm20) cc_final: 0.8095 (pm20) REVERT: A 190 MET cc_start: 0.8506 (tmm) cc_final: 0.8268 (tmm) REVERT: A 335 GLN cc_start: 0.7550 (tp40) cc_final: 0.6621 (tt0) REVERT: A 533 MET cc_start: 0.7384 (ttt) cc_final: 0.6591 (ttt) REVERT: B 30 PRO cc_start: 0.9388 (Cg_exo) cc_final: 0.8869 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8358 (m-40) cc_final: 0.7890 (m110) REVERT: B 36 MET cc_start: 0.9050 (mmm) cc_final: 0.8797 (mmm) REVERT: B 39 TYR cc_start: 0.8071 (m-80) cc_final: 0.7616 (m-10) REVERT: B 48 GLU cc_start: 0.8297 (pm20) cc_final: 0.7928 (pm20) REVERT: B 119 VAL cc_start: 0.8730 (m) cc_final: 0.8429 (m) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1332 time to fit residues: 30.9123 Evaluate side-chains 163 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.135336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107310 restraints weight = 8528.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110776 restraints weight = 4960.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113224 restraints weight = 3381.751| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4335 Z= 0.256 Angle : 0.743 9.352 5898 Z= 0.376 Chirality : 0.041 0.177 696 Planarity : 0.004 0.044 719 Dihedral : 4.007 14.890 590 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.37), residues: 541 helix: 2.20 (0.26), residues: 370 sheet: -0.12 (0.75), residues: 43 loop : -1.15 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 42 HIS 0.003 0.001 HIS A 32 PHE 0.020 0.001 PHE A 292 TYR 0.017 0.001 TYR A 318 ARG 0.004 0.001 ARG A 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8579 (t80) cc_final: 0.8300 (t80) REVERT: A 29 TYR cc_start: 0.9178 (m-10) cc_final: 0.8895 (m-80) REVERT: A 111 MET cc_start: 0.8409 (mmm) cc_final: 0.7922 (mmm) REVERT: A 119 GLU cc_start: 0.8382 (pm20) cc_final: 0.8112 (pm20) REVERT: A 190 MET cc_start: 0.8514 (tmm) cc_final: 0.8247 (tmm) REVERT: A 312 MET cc_start: 0.8476 (tpp) cc_final: 0.8260 (tpp) REVERT: A 335 GLN cc_start: 0.7527 (tp40) cc_final: 0.6638 (tt0) REVERT: A 393 MET cc_start: 0.7583 (mmm) cc_final: 0.7290 (mmt) REVERT: A 533 MET cc_start: 0.7416 (ttt) cc_final: 0.6551 (ttt) REVERT: B 30 PRO cc_start: 0.9424 (Cg_exo) cc_final: 0.9013 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8407 (m-40) cc_final: 0.7813 (m-40) REVERT: B 36 MET cc_start: 0.9016 (mmm) cc_final: 0.8732 (mmm) REVERT: B 38 TRP cc_start: 0.8497 (m100) cc_final: 0.8033 (m100) REVERT: B 119 VAL cc_start: 0.8760 (m) cc_final: 0.8441 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1389 time to fit residues: 31.8549 Evaluate side-chains 161 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108345 restraints weight = 8714.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111871 restraints weight = 5040.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114364 restraints weight = 3432.825| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4335 Z= 0.249 Angle : 0.756 8.919 5898 Z= 0.382 Chirality : 0.041 0.231 696 Planarity : 0.004 0.043 719 Dihedral : 4.063 14.840 590 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % 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: 1.74 (0.36), residues: 541 helix: 2.12 (0.26), residues: 371 sheet: -0.20 (0.72), residues: 43 loop : -1.32 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 37 HIS 0.003 0.001 HIS A 32 PHE 0.017 0.001 PHE B 70 TYR 0.015 0.001 TYR A 318 ARG 0.003 0.001 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.37 seconds wall clock time: 28 minutes 24.01 seconds (1704.01 seconds total)