Starting phenix.real_space_refine on Thu Mar 6 00:47:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c02_16353/03_2025/8c02_16353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c02_16353/03_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_16353/03_2025/8c02_16353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c02_16353/03_2025/8c02_16353.map" model { file = "/net/cci-nas-00/data/ceres_data/8c02_16353/03_2025/8c02_16353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c02_16353/03_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-5624/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: 3.07, per 1000 atoms: 0.72 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 523.1 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: 0.43 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: 1.25 Time building geometry restraints manager: 1.32 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- 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 : 0.806 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: 0.1531 time to fit residues: 37.7163 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 : 0.487 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109715 restraints weight = 8695.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113181 restraints weight = 5019.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115599 restraints weight = 3449.222| |-----------------------------------------------------------------------------| 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 : 0.441 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: 0.8225 (mtm-85) cc_final: 0.7998 (mtm-85) REVERT: A 180 ILE cc_start: 0.8282 (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: 0.8099 (m-40) cc_final: 0.7609 (m110) REVERT: B 38 TRP cc_start: 0.8297 (m100) cc_final: 0.7987 (m100) REVERT: B 70 PHE cc_start: 0.7748 (m-10) cc_final: 0.7414 (m-80) REVERT: B 85 MET cc_start: 0.7838 (mmp) cc_final: 0.7636 (mmp) REVERT: B 92 ASP cc_start: 0.7331 (m-30) cc_final: 0.6863 (m-30) REVERT: B 108 TRP cc_start: 0.8135 (t-100) cc_final: 0.7339 (t-100) REVERT: B 117 THR cc_start: 0.8808 (p) cc_final: 0.8549 (t) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1433 time to fit residues: 35.9712 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 : 0.480 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 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 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 = 0.3773 r_free = 0.3773 target = 0.137187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109240 restraints weight = 8604.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112785 restraints weight = 4844.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115201 restraints weight = 3262.056| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4335 Z= 0.214 Angle : 0.635 9.082 5898 Z= 0.327 Chirality : 0.040 0.161 696 Planarity : 0.004 0.045 719 Dihedral : 3.945 16.932 590 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % 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 (0.36), residues: 541 helix: 2.36 (0.26), residues: 371 sheet: -0.18 (0.83), residues: 38 loop : -1.42 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE A 292 TYR 0.018 0.002 TYR B 62 ARG 0.005 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 : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8815 (t80) cc_final: 0.8544 (t80) REVERT: A 29 TYR cc_start: 0.9288 (m-10) cc_final: 0.9033 (m-10) REVERT: A 79 ILE cc_start: 0.8990 (mm) cc_final: 0.8764 (tp) REVERT: A 179 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8076 (ttm110) REVERT: A 180 ILE cc_start: 0.8299 (mm) cc_final: 0.8069 (mm) REVERT: A 290 GLU cc_start: 0.8650 (pm20) cc_final: 0.8439 (pm20) REVERT: A 312 MET cc_start: 0.8553 (tpp) cc_final: 0.7368 (tpp) REVERT: A 495 VAL cc_start: 0.9560 (m) cc_final: 0.9359 (m) REVERT: A 536 ILE cc_start: 0.8253 (mm) cc_final: 0.8038 (mm) REVERT: B 34 ASN cc_start: 0.8179 (m-40) cc_final: 0.7671 (m110) REVERT: B 36 MET cc_start: 0.8968 (mmm) cc_final: 0.8760 (mmm) REVERT: B 38 TRP cc_start: 0.8206 (m100) cc_final: 0.7935 (m100) REVERT: B 92 ASP cc_start: 0.7280 (m-30) cc_final: 0.6751 (m-30) REVERT: B 108 TRP cc_start: 0.8364 (t-100) cc_final: 0.7798 (t-100) REVERT: B 119 VAL cc_start: 0.8906 (m) cc_final: 0.8610 (m) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1461 time to fit residues: 34.9432 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 : 0.438 ------------------------------------------------------------------------------- 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: 0.0000 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109477 restraints weight = 8724.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113060 restraints weight = 4876.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115491 restraints weight = 3273.878| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4335 Z= 0.202 Angle : 0.623 8.725 5898 Z= 0.319 Chirality : 0.040 0.146 696 Planarity : 0.004 0.051 719 Dihedral : 3.858 15.452 590 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.22 % Allowed : 4.41 % 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: 2.19 (0.36), residues: 541 helix: 2.49 (0.26), residues: 370 sheet: 0.11 (0.86), residues: 38 loop : -1.26 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 32 PHE 0.019 0.001 PHE B 70 TYR 0.012 0.001 TYR B 62 ARG 0.005 0.001 ARG B 74 *********************** 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 188 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8740 (t80) cc_final: 0.8443 (t80) REVERT: A 64 TYR cc_start: 0.8744 (t80) cc_final: 0.8464 (t80) REVERT: A 111 MET cc_start: 0.8256 (mmm) cc_final: 0.7892 (mmm) REVERT: A 119 GLU cc_start: 0.8046 (pm20) cc_final: 0.7782 (pm20) REVERT: A 180 ILE cc_start: 0.8336 (mm) cc_final: 0.8108 (mm) REVERT: A 290 GLU cc_start: 0.8659 (pm20) cc_final: 0.8441 (pm20) REVERT: A 312 MET cc_start: 0.8408 (tpp) cc_final: 0.7445 (tpp) REVERT: A 335 GLN cc_start: 0.7480 (tp40) cc_final: 0.6635 (tt0) REVERT: A 485 ILE cc_start: 0.8852 (mp) cc_final: 0.8305 (mt) REVERT: B 34 ASN cc_start: 0.8123 (m-40) cc_final: 0.7719 (m-40) REVERT: B 36 MET cc_start: 0.9015 (mmm) cc_final: 0.8797 (mmm) REVERT: B 46 GLU cc_start: 0.7345 (pp20) cc_final: 0.7086 (pp20) REVERT: B 92 ASP cc_start: 0.7263 (m-30) cc_final: 0.7038 (m-30) REVERT: B 108 TRP cc_start: 0.8437 (t-100) cc_final: 0.7987 (t-100) REVERT: B 119 VAL cc_start: 0.8859 (m) cc_final: 0.8445 (m) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1451 time to fit residues: 34.4028 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 : 0.453 ------------------------------------------------------------------------------- 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: 0.6980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 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 = 0.3760 r_free = 0.3760 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109533 restraints weight = 8772.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112812 restraints weight = 5050.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114947 restraints weight = 3439.848| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4335 Z= 0.216 Angle : 0.657 8.447 5898 Z= 0.335 Chirality : 0.040 0.147 696 Planarity : 0.004 0.032 719 Dihedral : 3.887 15.588 590 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % 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: 2.26 (0.37), residues: 541 helix: 2.50 (0.26), residues: 370 sheet: 0.29 (0.85), residues: 38 loop : -1.11 (0.53), 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 0.006 0.001 PHE B 70 TYR 0.015 0.001 TYR B 62 ARG 0.006 0.001 ARG B 21 *********************** 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 189 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.574 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: 0.8722 (t80) cc_final: 0.8398 (t80) REVERT: A 29 TYR cc_start: 0.9185 (m-10) cc_final: 0.8778 (m-80) REVERT: A 111 MET cc_start: 0.8150 (mmm) cc_final: 0.7804 (mmm) REVERT: A 119 GLU cc_start: 0.8049 (pm20) cc_final: 0.7827 (pm20) REVERT: A 180 ILE cc_start: 0.8230 (mm) cc_final: 0.7974 (mm) REVERT: A 290 GLU cc_start: 0.8521 (pm20) cc_final: 0.8189 (pm20) REVERT: A 312 MET cc_start: 0.8314 (tpp) cc_final: 0.8062 (tpt) REVERT: A 335 GLN cc_start: 0.7554 (tp40) cc_final: 0.6458 (tt0) REVERT: A 536 ILE cc_start: 0.8070 (mm) cc_final: 0.7867 (mm) REVERT: B 34 ASN cc_start: 0.8248 (m-40) cc_final: 0.7892 (m110) REVERT: B 36 MET cc_start: 0.9050 (mmm) cc_final: 0.8816 (mmm) REVERT: B 92 ASP cc_start: 0.7291 (m-30) cc_final: 0.7088 (m-30) REVERT: B 119 VAL cc_start: 0.8830 (m) cc_final: 0.8397 (m) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1591 time to fit residues: 38.6526 Evaluate side-chains 165 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.137689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111608 restraints weight = 8586.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114887 restraints weight = 4984.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.117117 restraints weight = 3413.341| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4335 Z= 0.202 Angle : 0.651 8.788 5898 Z= 0.333 Chirality : 0.039 0.144 696 Planarity : 0.004 0.033 719 Dihedral : 3.861 14.975 590 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: 2.22 (0.37), residues: 541 helix: 2.45 (0.26), residues: 370 sheet: 0.18 (0.78), residues: 43 loop : -1.09 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 108 HIS 0.004 0.001 HIS A 32 PHE 0.011 0.001 PHE A 292 TYR 0.013 0.001 TYR B 110 ARG 0.005 0.001 ARG B 21 *********************** 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 190 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8660 (t80) cc_final: 0.8417 (t80) REVERT: A 29 TYR cc_start: 0.9211 (m-10) cc_final: 0.8899 (m-80) REVERT: A 30 LEU cc_start: 0.9432 (tp) cc_final: 0.9141 (tt) REVERT: A 64 TYR cc_start: 0.8753 (t80) cc_final: 0.8465 (t80) REVERT: A 111 MET cc_start: 0.8247 (mmm) cc_final: 0.7900 (mmm) REVERT: A 119 GLU cc_start: 0.8165 (pm20) cc_final: 0.7871 (pm20) REVERT: A 180 ILE cc_start: 0.8131 (mm) cc_final: 0.7844 (mm) REVERT: A 190 MET cc_start: 0.8738 (tmm) cc_final: 0.8484 (tmm) REVERT: A 290 GLU cc_start: 0.8581 (pm20) cc_final: 0.8332 (pm20) REVERT: A 293 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8418 (ptp-170) REVERT: A 335 GLN cc_start: 0.7685 (tp40) cc_final: 0.6744 (tt0) REVERT: A 533 MET cc_start: 0.7712 (mmm) cc_final: 0.7365 (ttt) REVERT: B 30 PRO cc_start: 0.9381 (Cg_exo) cc_final: 0.8871 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8216 (m-40) cc_final: 0.7812 (m110) REVERT: B 36 MET cc_start: 0.9054 (mmm) cc_final: 0.8820 (mmm) REVERT: B 39 TYR cc_start: 0.7928 (m-80) cc_final: 0.7464 (m-80) REVERT: B 72 ILE cc_start: 0.8250 (tp) cc_final: 0.8025 (tp) REVERT: B 119 VAL cc_start: 0.8786 (m) cc_final: 0.8471 (m) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1391 time to fit residues: 33.6533 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 : 0.443 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** B 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111377 restraints weight = 9062.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114981 restraints weight = 5141.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117561 restraints weight = 3457.143| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4335 Z= 0.201 Angle : 0.669 8.609 5898 Z= 0.338 Chirality : 0.040 0.139 696 Planarity : 0.004 0.034 719 Dihedral : 3.851 14.821 590 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.36), residues: 541 helix: 2.34 (0.26), residues: 370 sheet: 0.25 (0.77), residues: 43 loop : -1.17 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 113 HIS 0.004 0.001 HIS A 32 PHE 0.015 0.001 PHE A 292 TYR 0.012 0.001 TYR B 62 ARG 0.005 0.001 ARG B 21 *********************** 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 : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8566 (t80) cc_final: 0.8360 (t80) REVERT: A 29 TYR cc_start: 0.9174 (m-10) cc_final: 0.8914 (m-80) REVERT: A 30 LEU cc_start: 0.9401 (tp) cc_final: 0.9128 (tt) REVERT: A 111 MET cc_start: 0.8314 (mmm) cc_final: 0.7875 (mmm) REVERT: A 119 GLU cc_start: 0.8407 (pm20) cc_final: 0.8120 (pm20) REVERT: A 190 MET cc_start: 0.8580 (tmm) cc_final: 0.8263 (tmm) REVERT: A 290 GLU cc_start: 0.8503 (pm20) cc_final: 0.8215 (pm20) REVERT: A 335 GLN cc_start: 0.7701 (tp40) cc_final: 0.6795 (tt0) REVERT: A 491 ILE cc_start: 0.8977 (mm) cc_final: 0.8671 (mm) REVERT: B 30 PRO cc_start: 0.9385 (Cg_exo) cc_final: 0.8777 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8303 (m-40) cc_final: 0.7919 (m110) REVERT: B 36 MET cc_start: 0.9085 (mmm) cc_final: 0.8808 (mmm) REVERT: B 46 GLU cc_start: 0.6983 (pp20) cc_final: 0.6707 (pp20) REVERT: B 97 TYR cc_start: 0.7754 (m-10) cc_final: 0.7547 (m-10) REVERT: B 119 VAL cc_start: 0.8762 (m) cc_final: 0.8416 (m) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1380 time to fit residues: 32.6821 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 : 0.443 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110673 restraints weight = 8755.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114151 restraints weight = 5081.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116614 restraints weight = 3461.123| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4275 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 : 0.715 8.972 5898 Z= 0.365 Chirality : 0.041 0.177 696 Planarity : 0.004 0.031 719 Dihedral : 4.036 17.939 590 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 : 0.22 % Allowed : 0.66 % 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: 2.05 (0.36), residues: 541 helix: 2.23 (0.26), residues: 370 sheet: 0.50 (0.77), residues: 42 loop : -0.96 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 38 HIS 0.004 0.001 HIS A 32 PHE 0.022 0.001 PHE A 292 TYR 0.014 0.001 TYR B 110 ARG 0.004 0.001 ARG B 21 *********************** 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 180 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8570 (t80) cc_final: 0.8312 (t80) REVERT: A 30 LEU cc_start: 0.9412 (tp) cc_final: 0.9122 (tt) REVERT: A 111 MET cc_start: 0.8313 (mmm) cc_final: 0.7875 (mmm) REVERT: A 119 GLU cc_start: 0.8422 (pm20) cc_final: 0.8117 (pm20) REVERT: A 190 MET cc_start: 0.8528 (tmm) cc_final: 0.8252 (tmm) REVERT: A 290 GLU cc_start: 0.8461 (pm20) cc_final: 0.8077 (pm20) REVERT: A 291 PRO cc_start: 0.8783 (Cg_exo) cc_final: 0.8557 (Cg_endo) REVERT: A 335 GLN cc_start: 0.7614 (tp40) cc_final: 0.6627 (tt0) REVERT: A 473 ASP cc_start: 0.9193 (t0) cc_final: 0.8791 (t0) REVERT: B 30 PRO cc_start: 0.9345 (Cg_exo) cc_final: 0.8801 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8336 (m-40) cc_final: 0.7854 (m110) REVERT: B 36 MET cc_start: 0.9063 (mmm) cc_final: 0.8789 (mmm) REVERT: B 38 TRP cc_start: 0.8048 (m100) cc_final: 0.7837 (m100) REVERT: B 72 ILE cc_start: 0.8287 (tp) cc_final: 0.8083 (tp) REVERT: B 105 MET cc_start: 0.8406 (mmp) cc_final: 0.8087 (mmp) REVERT: B 119 VAL cc_start: 0.8783 (m) cc_final: 0.8475 (m) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1428 time to fit residues: 33.0541 Evaluate side-chains 158 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112708 restraints weight = 8526.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116036 restraints weight = 5032.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118406 restraints weight = 3486.429| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4335 Z= 0.236 Angle : 0.720 9.304 5898 Z= 0.368 Chirality : 0.041 0.151 696 Planarity : 0.004 0.041 719 Dihedral : 4.125 20.310 590 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.37), residues: 541 helix: 2.21 (0.26), residues: 370 sheet: 0.74 (0.75), residues: 40 loop : -0.84 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.003 0.001 HIS A 535 PHE 0.007 0.001 PHE A 541 TYR 0.014 0.001 TYR A 318 ARG 0.006 0.001 ARG B 47 *********************** 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 177 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8538 (t80) cc_final: 0.8330 (t80) REVERT: A 111 MET cc_start: 0.8130 (mmm) cc_final: 0.7765 (mmm) REVERT: A 119 GLU cc_start: 0.8361 (pm20) cc_final: 0.8088 (pm20) REVERT: A 190 MET cc_start: 0.8602 (tmm) cc_final: 0.8294 (tmm) REVERT: A 290 GLU cc_start: 0.8606 (pm20) cc_final: 0.7737 (pm20) REVERT: A 335 GLN cc_start: 0.7580 (tp40) cc_final: 0.6602 (tt0) REVERT: B 30 PRO cc_start: 0.9318 (Cg_exo) cc_final: 0.8867 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8288 (m-40) cc_final: 0.7894 (m110) REVERT: B 36 MET cc_start: 0.9110 (mmm) cc_final: 0.8855 (mmm) REVERT: B 119 VAL cc_start: 0.8848 (m) cc_final: 0.8521 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1430 time to fit residues: 32.5250 Evaluate side-chains 154 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 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 ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112414 restraints weight = 8467.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115742 restraints weight = 5016.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118068 restraints weight = 3473.439| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4335 Z= 0.246 Angle : 0.736 9.388 5898 Z= 0.376 Chirality : 0.041 0.153 696 Planarity : 0.004 0.031 719 Dihedral : 4.116 18.784 590 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % 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: 2.12 (0.37), residues: 541 helix: 2.25 (0.26), residues: 370 sheet: 0.40 (0.77), residues: 41 loop : -0.77 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 470 HIS 0.004 0.001 HIS A 32 PHE 0.029 0.001 PHE A 292 TYR 0.017 0.001 TYR A 318 ARG 0.005 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 177 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8551 (t80) cc_final: 0.8342 (t80) REVERT: A 111 MET cc_start: 0.8135 (mmm) cc_final: 0.7759 (mmm) REVERT: A 119 GLU cc_start: 0.8393 (pm20) cc_final: 0.8107 (pm20) REVERT: A 190 MET cc_start: 0.8545 (tmm) cc_final: 0.8289 (tmm) REVERT: A 290 GLU cc_start: 0.8647 (pm20) cc_final: 0.8446 (pm20) REVERT: A 312 MET cc_start: 0.8074 (tpt) cc_final: 0.7865 (mmp) REVERT: A 324 PHE cc_start: 0.7747 (m-10) cc_final: 0.7320 (m-10) REVERT: A 325 ASP cc_start: 0.3061 (p0) cc_final: 0.2714 (p0) REVERT: A 335 GLN cc_start: 0.7515 (tp40) cc_final: 0.6635 (tt0) REVERT: A 393 MET cc_start: 0.7225 (mmm) cc_final: 0.6929 (mmt) REVERT: A 533 MET cc_start: 0.7394 (ttt) cc_final: 0.6672 (ttt) REVERT: B 30 PRO cc_start: 0.9353 (Cg_exo) cc_final: 0.9025 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8308 (m-40) cc_final: 0.7836 (m-40) REVERT: B 39 TYR cc_start: 0.7368 (m-10) cc_final: 0.7100 (m-10) REVERT: B 45 LYS cc_start: 0.6694 (pttm) cc_final: 0.6487 (pptt) REVERT: B 48 GLU cc_start: 0.7940 (pm20) cc_final: 0.7660 (pm20) REVERT: B 119 VAL cc_start: 0.8838 (m) cc_final: 0.8504 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1377 time to fit residues: 31.3196 Evaluate side-chains 155 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109604 restraints weight = 8655.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113046 restraints weight = 5193.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115435 restraints weight = 3650.943| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4335 Z= 0.248 Angle : 0.752 9.356 5898 Z= 0.386 Chirality : 0.041 0.147 696 Planarity : 0.004 0.035 719 Dihedral : 4.107 16.903 590 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.37), residues: 541 helix: 2.25 (0.26), residues: 370 sheet: 0.51 (0.77), residues: 40 loop : -0.80 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 113 HIS 0.003 0.001 HIS A 32 PHE 0.028 0.002 PHE A 292 TYR 0.013 0.001 TYR A 318 ARG 0.005 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.03 seconds wall clock time: 32 minutes 28.57 seconds (1948.57 seconds total)