Starting phenix.real_space_refine on Wed Jul 23 08:44:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.map" model { file = "/net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9luo_63400/07_2025/9luo_63400.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 13 5.16 5 C 1617 2.51 5 N 436 2.21 5 O 474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2540 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 534 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 3 Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 907 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "D" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1099 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Time building chain proxies: 3.36, per 1000 atoms: 1.32 Number of scatterers: 2540 At special positions: 0 Unit cell: (62.5884, 82.7061, 87.1767, 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 13 16.00 O 474 8.00 N 436 7.00 C 1617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 271.3 milliseconds 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 79.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.560A pdb=" N ALA A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.066A pdb=" N LEU A 334 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.087A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 537 through 547 Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.649A pdb=" N LEU C 35 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 68 through 79 removed outlier: 3.707A pdb=" N TRP C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.574A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 122 through 141 removed outlier: 3.555A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 141 " --> pdb=" O TYR C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 49 through 68 Processing helix chain 'D' and resid 89 through 103 removed outlier: 3.632A pdb=" N LYS D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.740A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.517A pdb=" N ASN D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 10 155 hydrogen bonds defined for protein. 456 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: 0.59 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 1 1.19 - 1.35: 828 1.35 - 1.50: 660 1.50 - 1.66: 1076 1.66 - 1.81: 20 Bond restraints: 2585 Sorted by residual: bond pdb=" CG PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sigma weight residual 1.503 1.041 0.462 3.40e-02 8.65e+02 1.85e+02 bond pdb=" N PRO C 114 " pdb=" CA PRO C 114 " ideal model delta sigma weight residual 1.468 1.522 -0.053 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CB PRO C 114 " pdb=" CG PRO C 114 " ideal model delta sigma weight residual 1.492 1.344 0.148 5.00e-02 4.00e+02 8.74e+00 bond pdb=" CA PRO C 114 " pdb=" CB PRO C 114 " ideal model delta sigma weight residual 1.536 1.490 0.045 1.69e-02 3.50e+03 7.23e+00 bond pdb=" N PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.80e+00 ... (remaining 2580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.64: 3475 6.64 - 13.29: 3 13.29 - 19.93: 0 19.93 - 26.58: 1 26.58 - 33.22: 2 Bond angle restraints: 3481 Sorted by residual: angle pdb=" N PRO C 114 " pdb=" CD PRO C 114 " pdb=" CG PRO C 114 " ideal model delta sigma weight residual 103.20 72.32 30.88 1.50e+00 4.44e-01 4.24e+02 angle pdb=" CA PRO C 114 " pdb=" CB PRO C 114 " pdb=" CG PRO C 114 " ideal model delta sigma weight residual 104.50 71.28 33.22 1.90e+00 2.77e-01 3.06e+02 angle pdb=" CB PRO C 114 " pdb=" CG PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sigma weight residual 106.10 127.68 -21.58 3.20e+00 9.77e-02 4.55e+01 angle pdb=" CA PRO C 114 " pdb=" N PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sigma weight residual 112.00 104.08 7.92 1.40e+00 5.10e-01 3.20e+01 angle pdb=" N PRO C 114 " pdb=" CA PRO C 114 " pdb=" CB PRO C 114 " ideal model delta sigma weight residual 102.33 95.83 6.50 1.18e+00 7.18e-01 3.04e+01 ... (remaining 3476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 1333 17.99 - 35.98: 172 35.98 - 53.97: 39 53.97 - 71.96: 17 71.96 - 89.95: 1 Dihedral angle restraints: 1562 sinusoidal: 641 harmonic: 921 Sorted by residual: dihedral pdb=" N PRO C 114 " pdb=" CG PRO C 114 " pdb=" CD PRO C 114 " pdb=" CB PRO C 114 " ideal model delta sinusoidal sigma weight residual -30.00 -86.81 56.81 1 1.50e+01 4.44e-03 1.93e+01 dihedral pdb=" CA PRO C 114 " pdb=" CB PRO C 114 " pdb=" CG PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sinusoidal sigma weight residual -38.00 -109.46 71.46 1 2.00e+01 2.50e-03 1.64e+01 dihedral pdb=" CA ILE C 83 " pdb=" C ILE C 83 " pdb=" N GLY C 84 " pdb=" CA GLY C 84 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 266 0.027 - 0.055: 84 0.055 - 0.082: 22 0.082 - 0.109: 16 0.109 - 0.136: 4 Chirality restraints: 392 Sorted by residual: chirality pdb=" CA ILE D 19 " pdb=" N ILE D 19 " pdb=" C ILE D 19 " pdb=" CB ILE D 19 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA PRO D 141 " pdb=" N PRO D 141 " pdb=" C PRO D 141 " pdb=" CB PRO D 141 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA THR C 81 " pdb=" N THR C 81 " pdb=" C THR C 81 " pdb=" CB THR C 81 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 389 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 336 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 337 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 140 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO D 141 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 43 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO D 44 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 44 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 44 " 0.025 5.00e-02 4.00e+02 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 214 2.74 - 3.28: 2497 3.28 - 3.82: 4161 3.82 - 4.36: 4550 4.36 - 4.90: 8131 Nonbonded interactions: 19553 Sorted by model distance: nonbonded pdb=" OD1 ASP D 105 " pdb=" OG1 THR D 108 " model vdw 2.201 3.040 nonbonded pdb=" O PHE A 540 " pdb=" OG SER A 544 " model vdw 2.255 3.040 nonbonded pdb=" NE2 GLN A 311 " pdb=" OE1 GLN A 542 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP C 48 " pdb=" OG1 THR C 51 " model vdw 2.318 3.040 nonbonded pdb=" NE2 HIS C 63 " pdb=" OE1 GLN C 67 " model vdw 2.376 3.120 ... (remaining 19548 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 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 : 0.010 0.462 2585 Z= 0.317 Angle : 1.050 33.222 3481 Z= 0.571 Chirality : 0.035 0.136 392 Planarity : 0.005 0.051 438 Dihedral : 17.374 89.954 958 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 20.22 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.51), residues: 302 helix: 1.64 (0.35), residues: 231 sheet: None (None), residues: 0 loop : -0.89 (0.83), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 168 HIS 0.002 0.001 HIS C 63 PHE 0.008 0.001 PHE D 110 TYR 0.003 0.000 TYR D 118 ARG 0.002 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.14622 ( 155) hydrogen bonds : angle 4.96339 ( 456) covalent geometry : bond 0.00995 ( 2585) covalent geometry : angle 1.04955 ( 3481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: C 114 PRO cc_start: 0.6337 (Cg_endo) cc_final: 0.6078 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1752 time to fit residues: 9.8628 Evaluate side-chains 46 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 542 GLN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.200534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.166811 restraints weight = 3108.915| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.08 r_work: 0.3933 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2585 Z= 0.159 Angle : 0.651 12.001 3481 Z= 0.321 Chirality : 0.039 0.129 392 Planarity : 0.005 0.053 438 Dihedral : 4.076 16.715 330 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 18.05 % Favored : 78.34 % 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: 1.46 (0.50), residues: 302 helix: 1.46 (0.34), residues: 233 sheet: None (None), residues: 0 loop : -0.59 (0.85), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.004 0.001 HIS C 79 PHE 0.008 0.001 PHE D 154 TYR 0.005 0.001 TYR C 136 ARG 0.003 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 155) hydrogen bonds : angle 3.98945 ( 456) covalent geometry : bond 0.00378 ( 2585) covalent geometry : angle 0.65120 ( 3481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 114 PRO cc_start: 0.6475 (OUTLIER) cc_final: 0.6218 (Cg_endo) REVERT: D 139 LYS cc_start: 0.7111 (mmtp) cc_final: 0.6898 (ttpp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 0.1406 time to fit residues: 8.8357 Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 PRO Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 151 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.203852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.170080 restraints weight = 3128.713| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.13 r_work: 0.3960 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2585 Z= 0.103 Angle : 0.582 12.362 3481 Z= 0.282 Chirality : 0.036 0.126 392 Planarity : 0.005 0.051 438 Dihedral : 3.994 17.245 330 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.53 % Allowed : 21.30 % Favored : 76.17 % 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: 1.98 (0.51), residues: 302 helix: 1.82 (0.34), residues: 233 sheet: None (None), residues: 0 loop : -0.34 (0.86), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.002 0.001 HIS C 63 PHE 0.007 0.001 PHE D 110 TYR 0.005 0.001 TYR C 107 ARG 0.002 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 155) hydrogen bonds : angle 3.69868 ( 456) covalent geometry : bond 0.00239 ( 2585) covalent geometry : angle 0.58236 ( 3481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 114 PRO cc_start: 0.6491 (Cg_endo) cc_final: 0.6261 (Cg_endo) REVERT: D 139 LYS cc_start: 0.7117 (mmtp) cc_final: 0.6916 (ttpp) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1441 time to fit residues: 8.8004 Evaluate side-chains 47 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.201903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.168565 restraints weight = 3137.986| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.10 r_work: 0.3942 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2585 Z= 0.119 Angle : 0.576 10.861 3481 Z= 0.280 Chirality : 0.037 0.133 392 Planarity : 0.004 0.053 438 Dihedral : 3.953 15.503 330 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 19.86 % Favored : 76.53 % 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: 1.97 (0.51), residues: 302 helix: 1.79 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -0.28 (0.89), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.002 0.001 HIS C 104 PHE 0.007 0.001 PHE D 154 TYR 0.004 0.001 TYR A 301 ARG 0.002 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 155) hydrogen bonds : angle 3.71388 ( 456) covalent geometry : bond 0.00284 ( 2585) covalent geometry : angle 0.57574 ( 3481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6954 (tt) REVERT: D 139 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6902 (ttpp) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1341 time to fit residues: 8.6240 Evaluate side-chains 55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.166959 restraints weight = 3178.684| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.07 r_work: 0.3934 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2585 Z= 0.131 Angle : 0.573 11.789 3481 Z= 0.280 Chirality : 0.038 0.132 392 Planarity : 0.004 0.052 438 Dihedral : 4.019 15.582 330 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.61 % Allowed : 20.22 % Favored : 76.17 % 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: 1.87 (0.51), residues: 302 helix: 1.73 (0.35), residues: 234 sheet: None (None), residues: 0 loop : -0.40 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS C 79 PHE 0.007 0.001 PHE A 304 TYR 0.005 0.001 TYR A 301 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 155) hydrogen bonds : angle 3.74547 ( 456) covalent geometry : bond 0.00317 ( 2585) covalent geometry : angle 0.57278 ( 3481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6981 (tt) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.1345 time to fit residues: 8.8847 Evaluate side-chains 56 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.167605 restraints weight = 3196.665| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.14 r_work: 0.3924 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2585 Z= 0.121 Angle : 0.554 11.861 3481 Z= 0.270 Chirality : 0.037 0.130 392 Planarity : 0.004 0.052 438 Dihedral : 3.959 15.161 330 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.97 % Allowed : 20.58 % Favored : 75.45 % 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 (0.51), residues: 302 helix: 1.75 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -0.45 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.003 0.001 HIS C 79 PHE 0.007 0.001 PHE C 120 TYR 0.004 0.001 TYR A 301 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03337 ( 155) hydrogen bonds : angle 3.70646 ( 456) covalent geometry : bond 0.00292 ( 2585) covalent geometry : angle 0.55396 ( 3481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6915 (tt) outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.1309 time to fit residues: 8.3217 Evaluate side-chains 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 2 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.202482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168580 restraints weight = 3239.564| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.17 r_work: 0.3941 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2585 Z= 0.105 Angle : 0.544 12.110 3481 Z= 0.262 Chirality : 0.036 0.131 392 Planarity : 0.004 0.052 438 Dihedral : 3.877 15.568 330 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.89 % Allowed : 21.66 % Favored : 75.45 % 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 (0.51), residues: 302 helix: 1.84 (0.35), residues: 234 sheet: None (None), residues: 0 loop : -0.44 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.002 0.001 HIS C 79 PHE 0.006 0.001 PHE D 154 TYR 0.004 0.001 TYR C 137 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 155) hydrogen bonds : angle 3.65042 ( 456) covalent geometry : bond 0.00248 ( 2585) covalent geometry : angle 0.54383 ( 3481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6933 (tt) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1359 time to fit residues: 8.3814 Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.167299 restraints weight = 3245.878| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.18 r_work: 0.3928 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2585 Z= 0.121 Angle : 0.560 12.672 3481 Z= 0.269 Chirality : 0.037 0.129 392 Planarity : 0.004 0.052 438 Dihedral : 3.944 14.556 330 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.25 % Allowed : 21.30 % Favored : 75.45 % 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 (0.51), residues: 302 helix: 1.73 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -0.47 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS C 79 PHE 0.006 0.001 PHE A 304 TYR 0.004 0.001 TYR C 136 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 155) hydrogen bonds : angle 3.69176 ( 456) covalent geometry : bond 0.00292 ( 2585) covalent geometry : angle 0.55953 ( 3481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6929 (tt) REVERT: D 167 GLN cc_start: 0.7182 (tp40) cc_final: 0.6140 (pm20) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1253 time to fit residues: 8.0782 Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.200967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167130 restraints weight = 3193.180| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.15 r_work: 0.3927 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2585 Z= 0.129 Angle : 0.578 13.013 3481 Z= 0.279 Chirality : 0.038 0.128 392 Planarity : 0.004 0.051 438 Dihedral : 3.971 14.832 330 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.25 % Allowed : 22.02 % Favored : 74.73 % 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: 1.73 (0.51), residues: 302 helix: 1.64 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -0.48 (0.88), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS C 79 PHE 0.007 0.001 PHE A 304 TYR 0.004 0.001 TYR A 301 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 155) hydrogen bonds : angle 3.77567 ( 456) covalent geometry : bond 0.00310 ( 2585) covalent geometry : angle 0.57792 ( 3481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6943 (tt) REVERT: D 167 GLN cc_start: 0.7208 (tp40) cc_final: 0.6145 (pm20) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.1231 time to fit residues: 8.0996 Evaluate side-chains 52 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 143 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.201013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167138 restraints weight = 3230.993| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.17 r_work: 0.3928 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2585 Z= 0.123 Angle : 0.575 13.252 3481 Z= 0.277 Chirality : 0.037 0.129 392 Planarity : 0.004 0.052 438 Dihedral : 3.952 14.554 330 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.89 % Allowed : 22.02 % Favored : 75.09 % 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: 1.78 (0.51), residues: 302 helix: 1.67 (0.34), residues: 234 sheet: None (None), residues: 0 loop : -0.47 (0.88), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS C 79 PHE 0.011 0.001 PHE D 170 TYR 0.004 0.001 TYR A 301 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 155) hydrogen bonds : angle 3.76485 ( 456) covalent geometry : bond 0.00295 ( 2585) covalent geometry : angle 0.57545 ( 3481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 90 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6950 (tt) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.1261 time to fit residues: 7.6351 Evaluate side-chains 51 residues out of total 277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.203839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172017 restraints weight = 3166.746| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.02 r_work: 0.3941 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2585 Z= 0.098 Angle : 0.546 12.972 3481 Z= 0.261 Chirality : 0.036 0.131 392 Planarity : 0.004 0.052 438 Dihedral : 3.804 15.376 330 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.53 % Allowed : 22.74 % Favored : 74.73 % 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: 2.01 (0.51), residues: 302 helix: 1.85 (0.35), residues: 234 sheet: None (None), residues: 0 loop : -0.41 (0.88), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS C 63 PHE 0.009 0.001 PHE D 170 TYR 0.005 0.001 TYR C 137 ARG 0.001 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 155) hydrogen bonds : angle 3.64213 ( 456) covalent geometry : bond 0.00224 ( 2585) covalent geometry : angle 0.54572 ( 3481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.13 seconds wall clock time: 32 minutes 46.06 seconds (1966.06 seconds total)