Starting phenix.real_space_refine on Wed Jul 23 11:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvl_34131/07_2025/7yvl_34131.cif" } resolution = 3.3 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= 0.028 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 14 5.16 5 C 2066 2.51 5 N 531 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1511 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.38, per 1000 atoms: 1.36 Number of scatterers: 3224 At special positions: 0 Unit cell: (81.18, 71.34, 95.12, 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 14 16.00 O 613 8.00 N 531 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.12 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: 0.68 Conformation dependent library (CDL) restraints added in 403.1 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.801A pdb=" N THR A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.601A pdb=" N ASP C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.105A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.843A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.707A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.605A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 5.617A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 95 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 113 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.990A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.545A pdb=" N VAL C 99 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 81 hydrogen bonds defined for protein. 174 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: 0.84 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 506 1.28 - 1.42: 949 1.42 - 1.56: 1839 1.56 - 1.71: 0 1.71 - 1.85: 16 Bond restraints: 3310 Sorted by residual: bond pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 1.331 1.533 -0.202 1.65e-02 3.67e+03 1.50e+02 bond pdb=" CA TYR C 93 " pdb=" C TYR C 93 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.26e-02 6.30e+03 9.99e+01 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.242 1.161 0.081 8.60e-03 1.35e+04 8.86e+01 bond pdb=" C TYR C 93 " pdb=" O TYR C 93 " ideal model delta sigma weight residual 1.234 1.137 0.097 1.19e-02 7.06e+03 6.67e+01 bond pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 1.539 1.495 0.044 5.40e-03 3.43e+04 6.58e+01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 4323 2.52 - 5.03: 163 5.03 - 7.55: 19 7.55 - 10.07: 4 10.07 - 12.59: 7 Bond angle restraints: 4516 Sorted by residual: angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 110.45 118.23 -7.78 7.80e-01 1.64e+00 9.95e+01 angle pdb=" O TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 123.27 134.47 -11.20 1.22e+00 6.72e-01 8.43e+01 angle pdb=" C TYR C 93 " pdb=" CA TYR C 93 " pdb=" CB TYR C 93 " ideal model delta sigma weight residual 109.72 97.13 12.59 1.66e+00 3.63e-01 5.75e+01 angle pdb=" CA TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 116.00 105.28 10.72 1.50e+00 4.44e-01 5.11e+01 angle pdb=" C SER C 97 " pdb=" CA SER C 97 " pdb=" CB SER C 97 " ideal model delta sigma weight residual 109.99 99.03 10.96 1.61e+00 3.86e-01 4.63e+01 ... (remaining 4511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1708 15.10 - 30.20: 180 30.20 - 45.29: 45 45.29 - 60.39: 9 60.39 - 75.49: 2 Dihedral angle restraints: 1944 sinusoidal: 727 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.49 -75.49 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual 123.40 141.60 -18.20 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C ILE A 102 " pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual -122.00 -139.22 17.22 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 487 0.159 - 0.317: 13 0.317 - 0.476: 2 0.476 - 0.635: 0 0.635 - 0.793: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 1.64 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA SER C 96 " pdb=" N SER C 96 " pdb=" C SER C 96 " pdb=" CB SER C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR C 95 " pdb=" N THR C 95 " pdb=" C THR C 95 " pdb=" CB THR C 95 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 500 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 103 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 485 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLY B 485 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 485 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL B 486 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 97 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C SER C 97 " -0.047 2.00e-02 2.50e+03 pdb=" O SER C 97 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 98 " 0.016 2.00e-02 2.50e+03 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 183 2.70 - 3.25: 3086 3.25 - 3.80: 4704 3.80 - 4.35: 6139 4.35 - 4.90: 10672 Nonbonded interactions: 24784 Sorted by model distance: nonbonded pdb=" O ASN B 388 " pdb=" OD1 ASN B 388 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.199 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.251 3.040 nonbonded pdb=" O ILE A 105 " pdb=" OH TYR C 38 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 92 " model vdw 2.366 3.040 ... (remaining 24779 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.520 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.000 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.011 0.202 3316 Z= 0.718 Angle : 1.426 53.281 4528 Z= 0.828 Chirality : 0.075 0.793 503 Planarity : 0.007 0.098 574 Dihedral : 12.977 71.126 1154 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.96 % Favored : 90.56 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % Cbeta Deviations : 1.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.33), residues: 413 helix: -4.88 (0.35), residues: 29 sheet: -2.71 (0.37), residues: 143 loop : -3.55 (0.32), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 55 HIS 0.008 0.002 HIS A 99 PHE 0.016 0.002 PHE A 106 TYR 0.020 0.002 TYR B 489 ARG 0.005 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.18743 ( 76) hydrogen bonds : angle 7.77322 ( 174) SS BOND : bond 0.03870 ( 6) SS BOND : angle 16.04889 ( 12) covalent geometry : bond 0.01093 ( 3310) covalent geometry : angle 1.16334 ( 4516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.337 Fit side-chains REVERT: A 17 THR cc_start: 0.7589 (m) cc_final: 0.7375 (m) REVERT: C 53 VAL cc_start: 0.8166 (t) cc_final: 0.7946 (t) REVERT: B 467 ASP cc_start: 0.7467 (p0) cc_final: 0.7161 (p0) outliers start: 5 outliers final: 1 residues processed: 121 average time/residue: 0.1990 time to fit residues: 27.9905 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN B 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108223 restraints weight = 6349.289| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.85 r_work: 0.3387 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3316 Z= 0.181 Angle : 0.753 13.855 4528 Z= 0.371 Chirality : 0.046 0.182 503 Planarity : 0.005 0.032 574 Dihedral : 5.360 43.468 462 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 5.98 % Allowed : 20.80 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.35), residues: 413 helix: -4.82 (0.39), residues: 22 sheet: -1.50 (0.41), residues: 134 loop : -2.78 (0.32), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 109 HIS 0.001 0.001 HIS B 519 PHE 0.010 0.001 PHE B 347 TYR 0.018 0.002 TYR C 93 ARG 0.003 0.001 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 76) hydrogen bonds : angle 5.73181 ( 174) SS BOND : bond 0.00560 ( 6) SS BOND : angle 2.58201 ( 12) covalent geometry : bond 0.00424 ( 3310) covalent geometry : angle 0.74218 ( 4516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7935 (mmtm) REVERT: A 59 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8096 (mttm) REVERT: C 62 ASN cc_start: 0.7348 (t0) cc_final: 0.7052 (t0) REVERT: C 72 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7354 (p) REVERT: B 357 ARG cc_start: 0.7870 (ttm170) cc_final: 0.6531 (mtt180) REVERT: B 467 ASP cc_start: 0.7769 (p0) cc_final: 0.7163 (p0) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.1845 time to fit residues: 22.1423 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104909 restraints weight = 6367.959| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.74 r_work: 0.3345 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3316 Z= 0.180 Angle : 0.659 9.313 4528 Z= 0.338 Chirality : 0.046 0.150 503 Planarity : 0.004 0.035 574 Dihedral : 4.825 23.836 460 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 6.27 % Allowed : 23.08 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.37), residues: 413 helix: -4.82 (0.35), residues: 20 sheet: -1.06 (0.42), residues: 146 loop : -2.47 (0.34), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 109 HIS 0.003 0.001 HIS A 99 PHE 0.008 0.002 PHE B 400 TYR 0.011 0.001 TYR C 93 ARG 0.003 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 76) hydrogen bonds : angle 5.45351 ( 174) SS BOND : bond 0.00693 ( 6) SS BOND : angle 2.45115 ( 12) covalent geometry : bond 0.00433 ( 3310) covalent geometry : angle 0.64810 ( 4516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8353 (mttm) REVERT: C 16 GLN cc_start: 0.6507 (mp10) cc_final: 0.6263 (mp10) REVERT: C 62 ASN cc_start: 0.7545 (t0) cc_final: 0.7202 (t0) REVERT: B 357 ARG cc_start: 0.7943 (ttm170) cc_final: 0.6350 (mtt180) REVERT: B 358 ILE cc_start: 0.8619 (mt) cc_final: 0.8351 (mm) outliers start: 22 outliers final: 17 residues processed: 94 average time/residue: 0.1530 time to fit residues: 17.3362 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106317 restraints weight = 6541.699| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.74 r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3316 Z= 0.110 Angle : 0.614 9.399 4528 Z= 0.311 Chirality : 0.044 0.142 503 Planarity : 0.004 0.031 574 Dihedral : 4.567 24.511 460 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 6.27 % Allowed : 23.08 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.37), residues: 413 helix: -4.87 (0.31), residues: 22 sheet: -0.42 (0.42), residues: 141 loop : -2.45 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 49 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE B 400 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 76) hydrogen bonds : angle 5.16190 ( 174) SS BOND : bond 0.00546 ( 6) SS BOND : angle 2.20472 ( 12) covalent geometry : bond 0.00258 ( 3310) covalent geometry : angle 0.60447 ( 4516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7463 (mt) REVERT: A 35 SER cc_start: 0.8650 (p) cc_final: 0.8445 (t) REVERT: C 16 GLN cc_start: 0.6554 (mp10) cc_final: 0.6230 (mp10) REVERT: C 62 ASN cc_start: 0.7572 (t0) cc_final: 0.7252 (t0) REVERT: B 357 ARG cc_start: 0.7900 (ttm170) cc_final: 0.6216 (mtt180) outliers start: 22 outliers final: 15 residues processed: 98 average time/residue: 0.1957 time to fit residues: 23.6755 Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 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 41 GLN B 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.119753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105272 restraints weight = 6494.509| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.69 r_work: 0.3357 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3316 Z= 0.132 Angle : 0.614 8.508 4528 Z= 0.311 Chirality : 0.044 0.182 503 Planarity : 0.004 0.031 574 Dihedral : 4.551 21.667 460 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 6.84 % Allowed : 25.36 % Favored : 67.81 % 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: -2.44 (0.37), residues: 413 helix: -4.90 (0.28), residues: 21 sheet: -0.16 (0.43), residues: 139 loop : -2.31 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 49 HIS 0.002 0.001 HIS B 519 PHE 0.007 0.001 PHE B 400 TYR 0.011 0.001 TYR B 365 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 76) hydrogen bonds : angle 5.09340 ( 174) SS BOND : bond 0.00516 ( 6) SS BOND : angle 1.86137 ( 12) covalent geometry : bond 0.00307 ( 3310) covalent geometry : angle 0.60733 ( 4516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7445 (mt) REVERT: C 16 GLN cc_start: 0.6594 (mp10) cc_final: 0.6200 (mp10) REVERT: C 62 ASN cc_start: 0.7650 (t0) cc_final: 0.7336 (t0) REVERT: B 357 ARG cc_start: 0.7914 (ttm170) cc_final: 0.6309 (mtt180) outliers start: 24 outliers final: 19 residues processed: 99 average time/residue: 0.1476 time to fit residues: 17.6496 Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 20 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 32 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 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105390 restraints weight = 6664.418| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.77 r_work: 0.3365 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3316 Z= 0.118 Angle : 0.606 8.339 4528 Z= 0.303 Chirality : 0.044 0.165 503 Planarity : 0.004 0.032 574 Dihedral : 4.429 20.720 460 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 7.12 % Allowed : 24.22 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.38), residues: 413 helix: -4.90 (0.31), residues: 21 sheet: 0.02 (0.44), residues: 139 loop : -2.20 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 PHE 0.007 0.001 PHE B 400 TYR 0.012 0.001 TYR C 93 ARG 0.003 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 76) hydrogen bonds : angle 5.06256 ( 174) SS BOND : bond 0.00879 ( 6) SS BOND : angle 1.86703 ( 12) covalent geometry : bond 0.00276 ( 3310) covalent geometry : angle 0.59920 ( 4516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7458 (mt) REVERT: C 16 GLN cc_start: 0.6633 (mp10) cc_final: 0.6220 (mp10) REVERT: C 62 ASN cc_start: 0.7648 (t0) cc_final: 0.7343 (t0) REVERT: B 357 ARG cc_start: 0.7984 (ttm170) cc_final: 0.6320 (mtt180) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.1931 time to fit residues: 23.8488 Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103077 restraints weight = 6509.883| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.65 r_work: 0.3323 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3316 Z= 0.187 Angle : 0.667 10.994 4528 Z= 0.340 Chirality : 0.046 0.172 503 Planarity : 0.004 0.034 574 Dihedral : 4.789 21.224 460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.49 % Rotamer: Outliers : 6.55 % Allowed : 26.78 % Favored : 66.67 % 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: -2.29 (0.38), residues: 413 helix: -4.91 (0.31), residues: 21 sheet: 0.02 (0.44), residues: 139 loop : -2.25 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.009 0.001 PHE B 400 TYR 0.009 0.001 TYR B 365 ARG 0.003 0.001 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 76) hydrogen bonds : angle 5.30425 ( 174) SS BOND : bond 0.00731 ( 6) SS BOND : angle 1.83724 ( 12) covalent geometry : bond 0.00431 ( 3310) covalent geometry : angle 0.66107 ( 4516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 GLN cc_start: 0.6637 (mp10) cc_final: 0.6202 (mp10) REVERT: C 62 ASN cc_start: 0.7823 (t0) cc_final: 0.7479 (t0) REVERT: C 71 ASN cc_start: 0.7941 (t0) cc_final: 0.7536 (t0) REVERT: B 357 ARG cc_start: 0.8021 (ttm170) cc_final: 0.6319 (mtt180) outliers start: 23 outliers final: 22 residues processed: 96 average time/residue: 0.1341 time to fit residues: 15.8304 Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103918 restraints weight = 6511.802| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.68 r_work: 0.3336 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.130 Angle : 0.643 9.787 4528 Z= 0.318 Chirality : 0.045 0.158 503 Planarity : 0.004 0.054 574 Dihedral : 4.554 19.915 460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 7.69 % Allowed : 26.21 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.38), residues: 413 helix: -4.85 (0.35), residues: 21 sheet: 0.15 (0.45), residues: 139 loop : -2.15 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR C 93 ARG 0.002 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 76) hydrogen bonds : angle 5.15568 ( 174) SS BOND : bond 0.00735 ( 6) SS BOND : angle 1.79378 ( 12) covalent geometry : bond 0.00302 ( 3310) covalent geometry : angle 0.63759 ( 4516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.373 Fit side-chains REVERT: C 16 GLN cc_start: 0.6663 (mp10) cc_final: 0.6219 (mp10) REVERT: C 62 ASN cc_start: 0.7804 (t0) cc_final: 0.7478 (t0) REVERT: B 357 ARG cc_start: 0.8006 (ttm170) cc_final: 0.6303 (mtt180) outliers start: 27 outliers final: 26 residues processed: 99 average time/residue: 0.1578 time to fit residues: 18.9492 Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102991 restraints weight = 6596.251| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.65 r_work: 0.3322 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3316 Z= 0.162 Angle : 0.702 15.758 4528 Z= 0.338 Chirality : 0.045 0.156 503 Planarity : 0.004 0.052 574 Dihedral : 4.719 19.937 460 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.75 % Favored : 92.01 % Rotamer: Outliers : 7.12 % Allowed : 27.64 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.39), residues: 413 helix: -4.62 (0.46), residues: 15 sheet: 0.13 (0.45), residues: 139 loop : -2.16 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.012 0.001 PHE B 342 TYR 0.009 0.001 TYR C 93 ARG 0.002 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 76) hydrogen bonds : angle 5.25757 ( 174) SS BOND : bond 0.00734 ( 6) SS BOND : angle 1.80655 ( 12) covalent geometry : bond 0.00380 ( 3310) covalent geometry : angle 0.69696 ( 4516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.6620 (mp10) cc_final: 0.6208 (mp10) REVERT: C 62 ASN cc_start: 0.7760 (t0) cc_final: 0.7431 (t0) REVERT: C 74 SER cc_start: 0.8360 (m) cc_final: 0.7772 (p) REVERT: B 357 ARG cc_start: 0.8020 (ttm170) cc_final: 0.6293 (mtt180) outliers start: 25 outliers final: 22 residues processed: 96 average time/residue: 0.2909 time to fit residues: 34.0313 Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103598 restraints weight = 6328.717| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.59 r_work: 0.3340 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.135 Angle : 0.652 8.837 4528 Z= 0.321 Chirality : 0.045 0.155 503 Planarity : 0.004 0.052 574 Dihedral : 4.533 18.850 460 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 6.84 % Allowed : 27.35 % Favored : 65.81 % 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: -1.94 (0.39), residues: 413 helix: -4.58 (0.48), residues: 15 sheet: 0.22 (0.45), residues: 139 loop : -2.07 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.001 0.001 HIS A 99 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR C 93 ARG 0.002 0.000 ARG C 63 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 76) hydrogen bonds : angle 5.18246 ( 174) SS BOND : bond 0.00667 ( 6) SS BOND : angle 1.73059 ( 12) covalent geometry : bond 0.00314 ( 3310) covalent geometry : angle 0.64691 ( 4516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: C 16 GLN cc_start: 0.6573 (mp10) cc_final: 0.6174 (mp10) REVERT: C 62 ASN cc_start: 0.7761 (t0) cc_final: 0.7458 (t0) REVERT: C 74 SER cc_start: 0.8303 (m) cc_final: 0.7689 (p) REVERT: B 357 ARG cc_start: 0.7968 (ttm170) cc_final: 0.6229 (mtt180) outliers start: 24 outliers final: 22 residues processed: 92 average time/residue: 0.2411 time to fit residues: 27.2307 Evaluate side-chains 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103683 restraints weight = 6490.983| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.60 r_work: 0.3337 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3316 Z= 0.130 Angle : 0.654 8.660 4528 Z= 0.321 Chirality : 0.045 0.154 503 Planarity : 0.004 0.050 574 Dihedral : 4.498 18.699 460 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 6.27 % Allowed : 28.21 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.39), residues: 413 helix: -4.56 (0.49), residues: 15 sheet: 0.18 (0.44), residues: 139 loop : -1.95 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.001 0.001 HIS A 99 PHE 0.009 0.001 PHE A 24 TYR 0.012 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 76) hydrogen bonds : angle 5.21067 ( 174) SS BOND : bond 0.00648 ( 6) SS BOND : angle 1.62833 ( 12) covalent geometry : bond 0.00303 ( 3310) covalent geometry : angle 0.64951 ( 4516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.75 seconds wall clock time: 64 minutes 35.22 seconds (3875.22 seconds total)