Starting phenix.real_space_refine on Wed Jun 4 21:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c02_16353/06_2025/8c02_16353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c02_16353/06_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_16353/06_2025/8c02_16353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c02_16353/06_2025/8c02_16353.map" model { file = "/net/cci-nas-00/data/ceres_data/8c02_16353/06_2025/8c02_16353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c02_16353/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.28, per 1000 atoms: 1.24 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: 2.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 0.97 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: 1.64 Time building geometry restraints manager: 2.91 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: 53.930 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 27.290 Find NCS groups from input model: 0.050 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:4.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.910 ------------------------------------------------------------------------------- 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 4336 Z= 0.188 Angle : 0.833 9.920 5900 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 Details of bonding type rmsd hydrogen bonds : bond 0.12218 ( 344) hydrogen bonds : angle 5.58573 ( 1014) SS BOND : bond 0.00047 ( 1) SS BOND : angle 2.16103 ( 2) covalent geometry : bond 0.00409 ( 4335) covalent geometry : angle 0.83181 ( 5898) *********************** 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 : 1.084 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: 0.2269 time to fit residues: 56.8033 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 : 0.582 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.134654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105957 restraints weight = 8689.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109280 restraints weight = 5094.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111629 restraints weight = 3559.255| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4336 Z= 0.167 Angle : 0.672 8.160 5900 Z= 0.343 Chirality : 0.041 0.163 696 Planarity : 0.005 0.066 719 Dihedral : 4.131 16.134 590 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 2.00 (0.36), residues: 541 helix: 2.36 (0.26), residues: 371 sheet: -0.11 (0.74), residues: 43 loop : -1.39 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 38 HIS 0.003 0.001 HIS A 32 PHE 0.006 0.001 PHE B 107 TYR 0.024 0.002 TYR A 29 ARG 0.006 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 344) hydrogen bonds : angle 4.58185 ( 1014) SS BOND : bond 0.00717 ( 1) SS BOND : angle 1.98604 ( 2) covalent geometry : bond 0.00369 ( 4335) covalent geometry : angle 0.67074 ( 5898) *********************** 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 193 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8773 (t80) cc_final: 0.8558 (t80) REVERT: A 111 MET cc_start: 0.8687 (tpt) cc_final: 0.8294 (mmm) REVERT: A 179 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8097 (mtm-85) REVERT: A 180 ILE cc_start: 0.8361 (mm) cc_final: 0.8157 (mm) REVERT: A 488 GLU cc_start: 0.7395 (tp30) cc_final: 0.7128 (tp30) REVERT: A 536 ILE cc_start: 0.8263 (mm) cc_final: 0.8047 (mm) REVERT: B 6 LEU cc_start: 0.8638 (pp) cc_final: 0.8341 (pp) REVERT: B 8 GLU cc_start: 0.7534 (mp0) cc_final: 0.5913 (mp0) REVERT: B 34 ASN cc_start: 0.8188 (m-40) cc_final: 0.7567 (m110) REVERT: B 38 TRP cc_start: 0.8382 (m100) cc_final: 0.8007 (m100) REVERT: B 92 ASP cc_start: 0.7348 (m-30) cc_final: 0.6935 (m-30) REVERT: B 117 THR cc_start: 0.8793 (p) cc_final: 0.8472 (t) REVERT: B 119 VAL cc_start: 0.9303 (t) cc_final: 0.9075 (t) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1508 time to fit residues: 37.0401 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 : 0.417 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.137302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109048 restraints weight = 8676.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112566 restraints weight = 4963.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115012 restraints weight = 3369.791| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4336 Z= 0.143 Angle : 0.636 9.007 5900 Z= 0.327 Chirality : 0.040 0.163 696 Planarity : 0.004 0.045 719 Dihedral : 3.932 16.829 590 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 2.03 (0.36), residues: 541 helix: 2.38 (0.26), residues: 370 sheet: -0.04 (0.81), residues: 38 loop : -1.31 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.009 0.001 PHE A 530 TYR 0.017 0.001 TYR B 62 ARG 0.006 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 344) hydrogen bonds : angle 4.37394 ( 1014) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.71497 ( 2) covalent geometry : bond 0.00319 ( 4335) covalent geometry : angle 0.63522 ( 5898) *********************** 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 : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8782 (t80) cc_final: 0.8511 (t80) REVERT: A 29 TYR cc_start: 0.9301 (m-10) cc_final: 0.9075 (m-10) REVERT: A 52 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8501 (mm-30) REVERT: A 79 ILE cc_start: 0.8980 (mm) cc_final: 0.8763 (tp) REVERT: A 179 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: A 180 ILE cc_start: 0.8215 (mm) cc_final: 0.7962 (mm) REVERT: A 312 MET cc_start: 0.8543 (tpp) cc_final: 0.7369 (tpp) REVERT: A 495 VAL cc_start: 0.9563 (m) cc_final: 0.9357 (m) REVERT: A 536 ILE cc_start: 0.8233 (mm) cc_final: 0.8028 (mm) REVERT: B 34 ASN cc_start: 0.8070 (m-40) cc_final: 0.7623 (m110) REVERT: B 38 TRP cc_start: 0.8113 (m100) cc_final: 0.7824 (m100) REVERT: B 70 PHE cc_start: 0.7685 (m-10) cc_final: 0.7295 (m-80) REVERT: B 92 ASP cc_start: 0.7617 (m-30) cc_final: 0.6992 (m-30) REVERT: B 97 TYR cc_start: 0.7815 (m-80) cc_final: 0.7229 (m-10) REVERT: B 108 TRP cc_start: 0.8446 (t-100) cc_final: 0.7694 (t-100) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1423 time to fit residues: 34.2938 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 : 0.467 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 B 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105568 restraints weight = 8611.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108936 restraints weight = 4956.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111291 restraints weight = 3371.013| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4336 Z= 0.175 Angle : 0.664 8.657 5900 Z= 0.341 Chirality : 0.040 0.145 696 Planarity : 0.004 0.038 719 Dihedral : 3.940 15.756 590 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.22 % Allowed : 4.63 % Favored : 95.15 % 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: 2.11 (0.36), residues: 541 helix: 2.37 (0.26), residues: 372 sheet: 0.29 (0.84), residues: 38 loop : -1.20 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 82 HIS 0.005 0.001 HIS A 507 PHE 0.008 0.001 PHE A 292 TYR 0.013 0.001 TYR B 62 ARG 0.004 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 344) hydrogen bonds : angle 4.45123 ( 1014) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.98004 ( 2) covalent geometry : bond 0.00388 ( 4335) covalent geometry : angle 0.66352 ( 5898) *********************** 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 194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8680 (t80) cc_final: 0.8332 (t80) REVERT: A 52 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8763 (mm-30) REVERT: A 111 MET cc_start: 0.8263 (mmm) cc_final: 0.7983 (mmm) REVERT: A 119 GLU cc_start: 0.8048 (pm20) cc_final: 0.7766 (pm20) REVERT: A 229 LYS cc_start: 0.8554 (tttt) cc_final: 0.8327 (tttt) REVERT: A 335 GLN cc_start: 0.7543 (tp40) cc_final: 0.6700 (tt0) REVERT: A 485 ILE cc_start: 0.8966 (mp) cc_final: 0.8476 (mt) REVERT: A 488 GLU cc_start: 0.7360 (tp30) cc_final: 0.6953 (tp30) REVERT: B 30 PRO cc_start: 0.9588 (Cg_exo) cc_final: 0.8815 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8499 (m-40) cc_final: 0.7990 (m110) REVERT: B 46 GLU cc_start: 0.7384 (pp20) cc_final: 0.7133 (pp20) REVERT: B 70 PHE cc_start: 0.7629 (m-10) cc_final: 0.7375 (m-80) REVERT: B 92 ASP cc_start: 0.7506 (m-30) cc_final: 0.7046 (m-30) REVERT: B 97 TYR cc_start: 0.7917 (m-80) cc_final: 0.7512 (m-10) REVERT: B 119 VAL cc_start: 0.8897 (m) cc_final: 0.8499 (m) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1616 time to fit residues: 40.2683 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 : 0.489 ------------------------------------------------------------------------------- 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: 0.5980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.135545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108673 restraints weight = 8708.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112204 restraints weight = 4879.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114602 restraints weight = 3254.429| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4336 Z= 0.143 Angle : 0.666 8.480 5900 Z= 0.336 Chirality : 0.039 0.149 696 Planarity : 0.004 0.032 719 Dihedral : 3.893 15.617 590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.59 % 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: 2.23 (0.36), residues: 541 helix: 2.45 (0.26), residues: 370 sheet: 0.52 (0.80), residues: 38 loop : -1.13 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 108 HIS 0.003 0.001 HIS A 32 PHE 0.009 0.001 PHE A 541 TYR 0.014 0.001 TYR B 62 ARG 0.007 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 344) hydrogen bonds : angle 4.32147 ( 1014) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.74705 ( 2) covalent geometry : bond 0.00315 ( 4335) covalent geometry : angle 0.66611 ( 5898) *********************** 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 187 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.554 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: 0.8698 (t80) cc_final: 0.8309 (t80) REVERT: A 111 MET cc_start: 0.8245 (mmm) cc_final: 0.7885 (mmm) REVERT: A 119 GLU cc_start: 0.8104 (pm20) cc_final: 0.7865 (pm20) REVERT: A 229 LYS cc_start: 0.8447 (tttt) cc_final: 0.8023 (tttt) REVERT: A 335 GLN cc_start: 0.7530 (tp40) cc_final: 0.6494 (tt0) REVERT: A 536 ILE cc_start: 0.8091 (mm) cc_final: 0.7885 (mm) REVERT: B 30 PRO cc_start: 0.9524 (Cg_exo) cc_final: 0.8820 (Cg_endo) REVERT: B 31 VAL cc_start: 0.8473 (m) cc_final: 0.8144 (m) REVERT: B 34 ASN cc_start: 0.8517 (m-40) cc_final: 0.7991 (m110) REVERT: B 70 PHE cc_start: 0.7378 (m-10) cc_final: 0.7178 (m-80) REVERT: B 92 ASP cc_start: 0.7426 (m-30) cc_final: 0.7032 (m-30) REVERT: B 97 TYR cc_start: 0.7852 (m-80) cc_final: 0.7463 (m-10) REVERT: B 115 GLN cc_start: 0.8249 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 119 VAL cc_start: 0.8797 (m) cc_final: 0.8413 (m) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.1539 time to fit residues: 36.3490 Evaluate side-chains 167 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 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 = 0.3747 r_free = 0.3747 target = 0.135345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108517 restraints weight = 8651.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111817 restraints weight = 5058.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113994 restraints weight = 3479.938| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4336 Z= 0.156 Angle : 0.684 8.752 5900 Z= 0.349 Chirality : 0.040 0.149 696 Planarity : 0.004 0.038 719 Dihedral : 3.895 15.315 590 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 2.23 (0.36), residues: 541 helix: 2.40 (0.26), residues: 370 sheet: 0.63 (0.75), residues: 43 loop : -1.05 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.011 0.001 PHE A 292 TYR 0.014 0.002 TYR B 110 ARG 0.005 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 344) hydrogen bonds : angle 4.35329 ( 1014) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.23835 ( 2) covalent geometry : bond 0.00348 ( 4335) covalent geometry : angle 0.68396 ( 5898) *********************** 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 180 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8656 (t80) cc_final: 0.8261 (t80) REVERT: A 52 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 111 MET cc_start: 0.8413 (mmm) cc_final: 0.8030 (mmm) REVERT: A 119 GLU cc_start: 0.8070 (pm20) cc_final: 0.7785 (pm20) REVERT: A 293 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8481 (ptp-110) REVERT: A 335 GLN cc_start: 0.7665 (tp40) cc_final: 0.6789 (tt0) REVERT: B 30 PRO cc_start: 0.9440 (Cg_exo) cc_final: 0.8816 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8457 (m-40) cc_final: 0.8000 (m110) REVERT: B 70 PHE cc_start: 0.7602 (m-10) cc_final: 0.7357 (m-80) REVERT: B 92 ASP cc_start: 0.7355 (m-30) cc_final: 0.6884 (m-30) REVERT: B 97 TYR cc_start: 0.7869 (m-80) cc_final: 0.7539 (m-10) REVERT: B 119 VAL cc_start: 0.8818 (m) cc_final: 0.8433 (m) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1401 time to fit residues: 31.9594 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 : 0.405 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3763 r_free = 0.3763 target = 0.136078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109203 restraints weight = 9003.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112738 restraints weight = 5096.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115171 restraints weight = 3435.538| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4336 Z= 0.157 Angle : 0.701 8.777 5900 Z= 0.356 Chirality : 0.040 0.157 696 Planarity : 0.004 0.039 719 Dihedral : 3.902 14.955 590 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % 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: 2.15 (0.36), residues: 541 helix: 2.28 (0.26), residues: 370 sheet: 0.95 (0.73), residues: 43 loop : -1.04 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 535 PHE 0.007 0.001 PHE A 541 TYR 0.015 0.001 TYR B 110 ARG 0.004 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 344) hydrogen bonds : angle 4.35187 ( 1014) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.36807 ( 2) covalent geometry : bond 0.00359 ( 4335) covalent geometry : angle 0.70069 ( 5898) *********************** 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 187 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8576 (t80) cc_final: 0.8243 (t80) REVERT: A 52 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 64 TYR cc_start: 0.8734 (t80) cc_final: 0.8528 (t80) REVERT: A 111 MET cc_start: 0.8372 (mmm) cc_final: 0.7972 (mmm) REVERT: A 119 GLU cc_start: 0.8206 (pm20) cc_final: 0.7888 (pm20) REVERT: A 194 GLN cc_start: 0.8285 (tt0) cc_final: 0.7688 (tt0) REVERT: A 335 GLN cc_start: 0.7576 (tp40) cc_final: 0.6671 (tt0) REVERT: B 21 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8365 (mmm-85) REVERT: B 30 PRO cc_start: 0.9475 (Cg_exo) cc_final: 0.8811 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8437 (m-40) cc_final: 0.7862 (m110) REVERT: B 70 PHE cc_start: 0.7489 (m-10) cc_final: 0.7264 (m-80) REVERT: B 92 ASP cc_start: 0.7251 (m-30) cc_final: 0.7047 (m-30) REVERT: B 97 TYR cc_start: 0.7843 (m-80) cc_final: 0.7533 (m-10) REVERT: B 119 VAL cc_start: 0.8779 (m) cc_final: 0.8363 (m) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1381 time to fit residues: 33.0313 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.4980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111378 restraints weight = 8658.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114738 restraints weight = 5171.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117109 restraints weight = 3594.018| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4336 Z= 0.153 Angle : 0.716 8.969 5900 Z= 0.367 Chirality : 0.041 0.187 696 Planarity : 0.004 0.036 719 Dihedral : 3.969 14.710 590 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.36), residues: 541 helix: 2.19 (0.26), residues: 370 sheet: 0.88 (0.72), residues: 43 loop : -1.08 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 108 HIS 0.006 0.001 HIS A 535 PHE 0.019 0.001 PHE A 292 TYR 0.018 0.002 TYR A 29 ARG 0.004 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 344) hydrogen bonds : angle 4.47698 ( 1014) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.34807 ( 2) covalent geometry : bond 0.00342 ( 4335) covalent geometry : angle 0.71591 ( 5898) *********************** 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 181 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 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: 0.8575 (t80) cc_final: 0.8223 (t80) REVERT: A 111 MET cc_start: 0.8320 (mmm) cc_final: 0.7916 (mmm) REVERT: A 119 GLU cc_start: 0.8382 (pm20) cc_final: 0.8090 (pm20) REVERT: A 190 MET cc_start: 0.8560 (tmm) cc_final: 0.8294 (tmm) REVERT: A 194 GLN cc_start: 0.8295 (tt0) cc_final: 0.7681 (tt0) REVERT: A 335 GLN cc_start: 0.7560 (tp40) cc_final: 0.6612 (tt0) REVERT: A 382 SER cc_start: 0.8442 (m) cc_final: 0.8054 (p) REVERT: B 30 PRO cc_start: 0.9321 (Cg_exo) cc_final: 0.8795 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8237 (m-40) cc_final: 0.7726 (m110) REVERT: B 70 PHE cc_start: 0.7547 (m-10) cc_final: 0.7345 (m-80) REVERT: B 97 TYR cc_start: 0.7836 (m-80) cc_final: 0.7490 (m-10) REVERT: B 119 VAL cc_start: 0.8743 (m) cc_final: 0.8444 (m) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1376 time to fit residues: 31.9613 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 : 0.474 ------------------------------------------------------------------------------- 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: 20.0000 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108417 restraints weight = 8898.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111982 restraints weight = 5101.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114479 restraints weight = 3473.117| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4336 Z= 0.165 Angle : 0.765 9.884 5900 Z= 0.389 Chirality : 0.041 0.181 696 Planarity : 0.004 0.030 719 Dihedral : 3.898 14.967 590 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 1.99 (0.36), residues: 541 helix: 2.18 (0.26), residues: 370 sheet: 0.92 (0.71), residues: 43 loop : -1.16 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.007 0.001 HIS A 535 PHE 0.016 0.001 PHE A 539 TYR 0.016 0.002 TYR A 29 ARG 0.007 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 344) hydrogen bonds : angle 4.43210 ( 1014) SS BOND : bond 0.00284 ( 1) SS BOND : angle 0.43647 ( 2) covalent geometry : bond 0.00386 ( 4335) covalent geometry : angle 0.76487 ( 5898) *********************** 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 172 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8528 (t80) cc_final: 0.8162 (t80) REVERT: A 111 MET cc_start: 0.8377 (mmm) cc_final: 0.7955 (mmm) REVERT: A 119 GLU cc_start: 0.8432 (pm20) cc_final: 0.8144 (pm20) REVERT: A 190 MET cc_start: 0.8563 (tmm) cc_final: 0.8292 (tmm) REVERT: A 194 GLN cc_start: 0.8309 (tt0) cc_final: 0.7713 (tt0) REVERT: A 335 GLN cc_start: 0.7608 (tp40) cc_final: 0.6718 (tt0) REVERT: A 473 ASP cc_start: 0.9360 (t0) cc_final: 0.9135 (t0) REVERT: B 30 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.8751 (Cg_endo) REVERT: B 31 VAL cc_start: 0.8656 (m) cc_final: 0.8224 (m) REVERT: B 34 ASN cc_start: 0.8281 (m-40) cc_final: 0.7646 (m110) REVERT: B 97 TYR cc_start: 0.7738 (m-80) cc_final: 0.7521 (m-10) REVERT: B 119 VAL cc_start: 0.8754 (m) cc_final: 0.8434 (m) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1395 time to fit residues: 30.6770 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 : 0.449 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.136052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108434 restraints weight = 8577.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111912 restraints weight = 4947.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114335 restraints weight = 3374.282| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4336 Z= 0.188 Angle : 0.799 11.706 5900 Z= 0.406 Chirality : 0.042 0.178 696 Planarity : 0.004 0.038 719 Dihedral : 4.092 15.984 590 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.42 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: 1.84 (0.36), residues: 541 helix: 2.10 (0.26), residues: 371 sheet: 0.76 (0.71), residues: 43 loop : -1.34 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 470 HIS 0.007 0.001 HIS A 535 PHE 0.031 0.002 PHE A 292 TYR 0.013 0.002 TYR A 29 ARG 0.008 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 344) hydrogen bonds : angle 4.58681 ( 1014) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.12098 ( 2) covalent geometry : bond 0.00439 ( 4335) covalent geometry : angle 0.79884 ( 5898) ********************** 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 175 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8671 (t80) cc_final: 0.8388 (t80) REVERT: A 111 MET cc_start: 0.8225 (mmm) cc_final: 0.7844 (mmm) REVERT: A 119 GLU cc_start: 0.8374 (pm20) cc_final: 0.8128 (pm20) REVERT: A 190 MET cc_start: 0.8543 (tmm) cc_final: 0.8256 (tmm) REVERT: A 194 GLN cc_start: 0.8376 (tt0) cc_final: 0.7753 (tt0) REVERT: A 335 GLN cc_start: 0.7555 (tp40) cc_final: 0.6670 (tt0) REVERT: A 393 MET cc_start: 0.7478 (mmm) cc_final: 0.7147 (mmt) REVERT: A 473 ASP cc_start: 0.9362 (t0) cc_final: 0.8851 (t0) REVERT: B 30 PRO cc_start: 0.9329 (Cg_exo) cc_final: 0.8846 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8286 (m-40) cc_final: 0.7674 (m110) REVERT: B 119 VAL cc_start: 0.8811 (m) cc_final: 0.8490 (m) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1324 time to fit residues: 29.6535 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 : 0.429 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 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** A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109599 restraints weight = 8637.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113235 restraints weight = 4996.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115660 restraints weight = 3410.137| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4336 Z= 0.169 Angle : 0.782 9.263 5900 Z= 0.394 Chirality : 0.041 0.142 696 Planarity : 0.004 0.028 719 Dihedral : 4.057 14.918 590 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % 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: 1.88 (0.36), residues: 541 helix: 2.12 (0.26), residues: 371 sheet: 0.88 (0.72), residues: 43 loop : -1.35 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 470 HIS 0.006 0.001 HIS A 535 PHE 0.020 0.002 PHE B 70 TYR 0.011 0.001 TYR A 501 ARG 0.010 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 344) hydrogen bonds : angle 4.51125 ( 1014) SS BOND : bond 0.00370 ( 1) SS BOND : angle 0.42783 ( 2) covalent geometry : bond 0.00392 ( 4335) covalent geometry : angle 0.78173 ( 5898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.29 seconds wall clock time: 37 minutes 50.21 seconds (2270.21 seconds total)