Starting phenix.real_space_refine on Fri May 9 23:13:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1b_33559/05_2025/7y1b_33559_neut.cif" } resolution = 3.23 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2587 2.51 5 N 698 2.21 5 O 836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4137 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 868 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "L" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1661 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 3.40, per 1000 atoms: 0.82 Number of scatterers: 4137 At special positions: 0 Unit cell: (76.44, 65.52, 107.52, 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 16 16.00 O 836 8.00 N 698 7.00 C 2587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 163 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 3.7% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.294A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 4.213A pdb=" N LYS H 84 " --> pdb=" O GLU H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'L' and resid 99 through 103 removed outlier: 4.095A pdb=" N VAL L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.964A pdb=" N THR A 186 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 28 through 31 removed outlier: 6.558A pdb=" N GLU H 29 " --> pdb=" O THR H 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 78 through 79 removed outlier: 6.687A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 53 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 125 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AA7, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AA8, first strand: chain 'H' and resid 174 through 177 Processing sheet with id=AA9, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.832A pdb=" N TYR L 106 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN L 57 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU L 66 " --> pdb=" O GLN L 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 134 through 138 removed outlier: 3.922A pdb=" N ASN L 157 " --> pdb=" O THR L 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 173 through 174 removed outlier: 6.278A pdb=" N HIS L 218 " --> pdb=" O SER L 223 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER L 223 " --> pdb=" O HIS L 218 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1331 1.34 - 1.46: 1049 1.46 - 1.58: 1832 1.58 - 1.70: 0 1.70 - 1.82: 21 Bond restraints: 4233 Sorted by residual: bond pdb=" CG PRO H 72 " pdb=" CD PRO H 72 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.29e+00 bond pdb=" CG PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.22e+00 bond pdb=" CZ ARG H 117 " pdb=" NH2 ARG H 117 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.07e+00 bond pdb=" CB PRO L 161 " pdb=" CG PRO L 161 " ideal model delta sigma weight residual 1.492 1.443 0.049 5.00e-02 4.00e+02 9.56e-01 bond pdb=" CB GLN H 25 " pdb=" CG GLN H 25 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 ... (remaining 4228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 5475 1.25 - 2.50: 227 2.50 - 3.75: 45 3.75 - 5.00: 13 5.00 - 6.24: 3 Bond angle restraints: 5763 Sorted by residual: angle pdb=" C TYR L 70 " pdb=" N VAL L 71 " pdb=" CA VAL L 71 " ideal model delta sigma weight residual 120.46 116.81 3.65 1.37e+00 5.33e-01 7.11e+00 angle pdb=" N TYR L 160 " pdb=" CA TYR L 160 " pdb=" C TYR L 160 " ideal model delta sigma weight residual 109.81 115.61 -5.80 2.21e+00 2.05e-01 6.88e+00 angle pdb=" N TYR L 70 " pdb=" CA TYR L 70 " pdb=" C TYR L 70 " ideal model delta sigma weight residual 108.23 104.68 3.55 1.38e+00 5.25e-01 6.63e+00 angle pdb=" CA TYR A 132 " pdb=" CB TYR A 132 " pdb=" CG TYR A 132 " ideal model delta sigma weight residual 113.90 109.57 4.33 1.80e+00 3.09e-01 5.80e+00 angle pdb=" N SER L 72 " pdb=" CA SER L 72 " pdb=" C SER L 72 " ideal model delta sigma weight residual 110.80 115.76 -4.96 2.13e+00 2.20e-01 5.43e+00 ... (remaining 5758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2277 17.56 - 35.12: 214 35.12 - 52.68: 39 52.68 - 70.24: 7 70.24 - 87.79: 3 Dihedral angle restraints: 2540 sinusoidal: 973 harmonic: 1567 Sorted by residual: dihedral pdb=" CA PRO H 170 " pdb=" C PRO H 170 " pdb=" N GLU H 171 " pdb=" CA GLU H 171 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR H 79 " pdb=" C TYR H 79 " pdb=" N ASN H 80 " pdb=" CA ASN H 80 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU H 102 " pdb=" C LEU H 102 " pdb=" N SER H 103 " pdb=" CA SER H 103 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 351 0.032 - 0.064: 210 0.064 - 0.095: 46 0.095 - 0.127: 37 0.127 - 0.159: 9 Chirality restraints: 653 Sorted by residual: chirality pdb=" CA ILE L 68 " pdb=" N ILE L 68 " pdb=" C ILE L 68 " pdb=" CB ILE L 68 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 650 not shown) Planarity restraints: 735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 167 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO A 168 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 132 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 133 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 71 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO H 72 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 72 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 72 " -0.020 5.00e-02 4.00e+02 ... (remaining 732 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1514 2.85 - 3.36: 3279 3.36 - 3.88: 6231 3.88 - 4.39: 7142 4.39 - 4.90: 13496 Nonbonded interactions: 31662 Sorted by model distance: nonbonded pdb=" O GLY H 156 " pdb=" OG SER H 157 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 179 " pdb=" OD2 ASP A 183 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS H 86 " pdb=" O SER H 104 " model vdw 2.349 3.120 nonbonded pdb=" O SER L 188 " pdb=" OG SER L 188 " model vdw 2.354 3.040 nonbonded pdb=" O SER L 97 " pdb=" OG SER L 97 " model vdw 2.371 3.040 ... (remaining 31657 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: 2.650 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.006 0.049 4238 Z= 0.240 Angle : 0.637 6.244 5773 Z= 0.341 Chirality : 0.047 0.159 653 Planarity : 0.005 0.060 735 Dihedral : 14.264 87.794 1519 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.42 (0.35), residues: 533 helix: -3.89 (1.04), residues: 12 sheet: -0.13 (0.31), residues: 258 loop : -1.65 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 66 HIS 0.005 0.001 HIS H 71 PHE 0.009 0.002 PHE L 155 TYR 0.022 0.002 TYR A 132 ARG 0.014 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.11059 ( 150) hydrogen bonds : angle 5.95813 ( 408) SS BOND : bond 0.00471 ( 5) SS BOND : angle 1.07550 ( 10) covalent geometry : bond 0.00572 ( 4233) covalent geometry : angle 0.63564 ( 5763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.504 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1908 time to fit residues: 12.5113 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109863 restraints weight = 5574.986| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.15 r_work: 0.3257 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4238 Z= 0.134 Angle : 0.615 7.723 5773 Z= 0.313 Chirality : 0.045 0.161 653 Planarity : 0.005 0.064 735 Dihedral : 4.643 19.094 578 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.63 % Allowed : 5.27 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.92 (0.36), residues: 533 helix: -3.65 (0.97), residues: 13 sheet: 0.20 (0.31), residues: 261 loop : -1.28 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.009 0.001 PHE H 189 TYR 0.014 0.001 TYR A 132 ARG 0.005 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 150) hydrogen bonds : angle 5.32637 ( 408) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.77452 ( 10) covalent geometry : bond 0.00331 ( 4233) covalent geometry : angle 0.61469 ( 5763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: H 128 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8454 (mm-40) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1765 time to fit residues: 11.9790 Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111982 restraints weight = 5498.711| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.13 r_work: 0.3297 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4238 Z= 0.111 Angle : 0.564 6.410 5773 Z= 0.286 Chirality : 0.044 0.158 653 Planarity : 0.005 0.062 735 Dihedral : 4.262 17.947 578 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.63 % Allowed : 8.65 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.73 (0.37), residues: 533 helix: -3.53 (0.92), residues: 14 sheet: 0.29 (0.31), residues: 258 loop : -1.08 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.007 0.001 PHE A 139 TYR 0.012 0.001 TYR A 132 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02490 ( 150) hydrogen bonds : angle 4.97775 ( 408) SS BOND : bond 0.00299 ( 5) SS BOND : angle 0.69106 ( 10) covalent geometry : bond 0.00268 ( 4233) covalent geometry : angle 0.56349 ( 5763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1633 time to fit residues: 10.8484 Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109186 restraints weight = 5557.653| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.21 r_work: 0.3273 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4238 Z= 0.128 Angle : 0.569 6.465 5773 Z= 0.289 Chirality : 0.044 0.154 653 Planarity : 0.005 0.061 735 Dihedral : 4.275 17.861 578 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.84 % Allowed : 10.55 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.56 (0.37), residues: 533 helix: -3.53 (0.90), residues: 14 sheet: 0.41 (0.32), residues: 259 loop : -0.97 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.007 0.001 PHE A 139 TYR 0.011 0.001 TYR L 70 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 150) hydrogen bonds : angle 4.95359 ( 408) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.71873 ( 10) covalent geometry : bond 0.00316 ( 4233) covalent geometry : angle 0.56853 ( 5763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.522 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1625 time to fit residues: 10.9696 Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 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 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118154 restraints weight = 5437.412| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.10 r_work: 0.3290 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4238 Z= 0.113 Angle : 0.547 6.124 5773 Z= 0.278 Chirality : 0.044 0.150 653 Planarity : 0.005 0.062 735 Dihedral : 4.138 17.714 578 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.84 % Allowed : 11.18 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.35 (0.37), residues: 533 helix: -3.48 (0.89), residues: 14 sheet: 0.58 (0.32), residues: 259 loop : -0.88 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.008 0.001 PHE A 139 TYR 0.010 0.001 TYR L 70 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02417 ( 150) hydrogen bonds : angle 4.84382 ( 408) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.64419 ( 10) covalent geometry : bond 0.00276 ( 4233) covalent geometry : angle 0.54727 ( 5763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.443 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1666 time to fit residues: 10.5472 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109043 restraints weight = 5578.340| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.17 r_work: 0.3231 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4238 Z= 0.185 Angle : 0.615 6.928 5773 Z= 0.312 Chirality : 0.045 0.150 653 Planarity : 0.005 0.062 735 Dihedral : 4.514 18.032 578 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.84 % Allowed : 12.66 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.42 (0.37), residues: 533 helix: -3.50 (0.86), residues: 14 sheet: 0.47 (0.32), residues: 259 loop : -0.84 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 138 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.002 PHE L 229 TYR 0.014 0.001 TYR L 70 ARG 0.007 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 150) hydrogen bonds : angle 5.17651 ( 408) SS BOND : bond 0.00365 ( 5) SS BOND : angle 0.79665 ( 10) covalent geometry : bond 0.00460 ( 4233) covalent geometry : angle 0.61414 ( 5763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.443 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1568 time to fit residues: 9.7332 Evaluate side-chains 45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115167 restraints weight = 5461.336| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.06 r_work: 0.3172 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4238 Z= 0.155 Angle : 0.591 6.915 5773 Z= 0.300 Chirality : 0.045 0.148 653 Planarity : 0.005 0.062 735 Dihedral : 4.419 18.009 578 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.84 % Allowed : 13.08 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.35 (0.37), residues: 533 helix: -3.48 (0.87), residues: 14 sheet: 0.51 (0.32), residues: 259 loop : -0.79 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.007 0.001 PHE L 229 TYR 0.012 0.001 TYR L 70 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 150) hydrogen bonds : angle 5.11908 ( 408) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.75882 ( 10) covalent geometry : bond 0.00385 ( 4233) covalent geometry : angle 0.59086 ( 5763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.493 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1579 time to fit residues: 9.9601 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109000 restraints weight = 5540.858| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.11 r_work: 0.3132 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4238 Z= 0.219 Angle : 0.652 7.545 5773 Z= 0.331 Chirality : 0.047 0.161 653 Planarity : 0.006 0.062 735 Dihedral : 4.738 18.484 578 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.63 % Allowed : 14.56 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.51 (0.37), residues: 533 helix: -3.60 (0.79), residues: 14 sheet: 0.37 (0.32), residues: 259 loop : -0.85 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 138 HIS 0.004 0.001 HIS H 71 PHE 0.009 0.002 PHE L 229 TYR 0.015 0.002 TYR L 70 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 150) hydrogen bonds : angle 5.40111 ( 408) SS BOND : bond 0.00399 ( 5) SS BOND : angle 0.88751 ( 10) covalent geometry : bond 0.00544 ( 4233) covalent geometry : angle 0.65121 ( 5763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.649 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.1607 time to fit residues: 9.8726 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.0070 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119817 restraints weight = 5291.424| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.03 r_work: 0.3300 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4238 Z= 0.099 Angle : 0.542 5.917 5773 Z= 0.276 Chirality : 0.043 0.158 653 Planarity : 0.005 0.062 735 Dihedral : 4.117 17.406 578 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.63 % Allowed : 14.77 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.21 (0.37), residues: 533 helix: -3.49 (0.91), residues: 14 sheet: 0.67 (0.33), residues: 258 loop : -0.76 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS H 71 PHE 0.009 0.001 PHE A 139 TYR 0.007 0.001 TYR L 70 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02341 ( 150) hydrogen bonds : angle 4.89042 ( 408) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.67384 ( 10) covalent geometry : bond 0.00236 ( 4233) covalent geometry : angle 0.54224 ( 5763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.453 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1740 time to fit residues: 10.4839 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 44 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118313 restraints weight = 5330.418| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.04 r_work: 0.3281 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4238 Z= 0.119 Angle : 0.559 5.964 5773 Z= 0.284 Chirality : 0.044 0.176 653 Planarity : 0.005 0.062 735 Dihedral : 4.182 17.062 578 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.42 % Allowed : 15.19 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.16 (0.38), residues: 533 helix: -3.52 (0.87), residues: 14 sheet: 0.72 (0.33), residues: 258 loop : -0.73 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.007 0.001 PHE A 139 TYR 0.009 0.001 TYR L 70 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02473 ( 150) hydrogen bonds : angle 4.90487 ( 408) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.66923 ( 10) covalent geometry : bond 0.00291 ( 4233) covalent geometry : angle 0.55905 ( 5763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.486 Fit side-chains REVERT: H 194 GLN cc_start: 0.7554 (pt0) cc_final: 0.7334 (tt0) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.1727 time to fit residues: 10.4664 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118837 restraints weight = 5319.858| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.04 r_work: 0.3287 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4238 Z= 0.115 Angle : 0.554 6.013 5773 Z= 0.281 Chirality : 0.044 0.172 653 Planarity : 0.005 0.059 735 Dihedral : 4.135 16.653 578 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.63 % Allowed : 15.19 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.12 (0.38), residues: 533 helix: -3.51 (0.87), residues: 14 sheet: 0.76 (0.33), residues: 258 loop : -0.72 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.001 PHE A 139 TYR 0.009 0.001 TYR L 70 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02432 ( 150) hydrogen bonds : angle 4.86389 ( 408) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.66809 ( 10) covalent geometry : bond 0.00282 ( 4233) covalent geometry : angle 0.55337 ( 5763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.29 seconds wall clock time: 42 minutes 49.50 seconds (2569.50 seconds total)