Starting phenix.real_space_refine on Wed Jul 23 19:45:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1b_33559/07_2025/7y1b_33559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1b_33559/07_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_33559/07_2025/7y1b_33559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1b_33559/07_2025/7y1b_33559.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1b_33559/07_2025/7y1b_33559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1b_33559/07_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-5711/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: 3.26, per 1000 atoms: 0.79 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: 0.90 Conformation dependent library (CDL) restraints added in 486.3 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: 0.50 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: 1.05 Time building geometry restraints manager: 1.11 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: 33.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.170 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.110 ------------------------------------------------------------------------------- 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 : 0.487 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1922 time to fit residues: 12.9660 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 : 0.851 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3488 r_free = 0.3488 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109757 restraints weight = 5567.403| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.13 r_work: 0.3255 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4238 Z= 0.139 Angle : 0.617 7.837 5773 Z= 0.314 Chirality : 0.046 0.162 653 Planarity : 0.005 0.064 735 Dihedral : 4.648 19.004 578 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.32 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: -0.93 (0.36), residues: 533 helix: -3.63 (0.98), residues: 13 sheet: 0.20 (0.31), residues: 261 loop : -1.30 (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 0.008 0.001 PHE A 139 TYR 0.014 0.001 TYR A 132 ARG 0.005 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02836 ( 150) hydrogen bonds : angle 5.33100 ( 408) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.82903 ( 10) covalent geometry : bond 0.00343 ( 4233) covalent geometry : angle 0.61631 ( 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 : 0.485 Fit side-chains revert: symmetry clash REVERT: H 128 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8456 (mm-40) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1699 time to fit residues: 11.5234 Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.127784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110028 restraints weight = 5520.026| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.15 r_work: 0.3272 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1226 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= 0.135 Angle : 0.590 6.987 5773 Z= 0.300 Chirality : 0.045 0.162 653 Planarity : 0.005 0.063 735 Dihedral : 4.454 18.411 578 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.63 % Allowed : 9.07 % Favored : 90.30 % 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: -0.81 (0.37), residues: 533 helix: -3.62 (0.84), residues: 14 sheet: 0.20 (0.31), residues: 259 loop : -1.10 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.001 PHE A 139 TYR 0.013 0.001 TYR A 132 ARG 0.006 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02695 ( 150) hydrogen bonds : angle 5.13131 ( 408) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.76168 ( 10) covalent geometry : bond 0.00332 ( 4233) covalent geometry : angle 0.59014 ( 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 : 0.457 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 0.2294 time to fit residues: 15.4659 Evaluate side-chains 51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3577 r_free = 0.3577 target = 0.134416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117116 restraints weight = 5422.472| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.12 r_work: 0.3279 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1367 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= 0.127 Angle : 0.574 6.475 5773 Z= 0.291 Chirality : 0.044 0.162 653 Planarity : 0.005 0.061 735 Dihedral : 4.331 18.426 578 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -0.62 (0.37), residues: 533 helix: -3.54 (0.85), residues: 14 sheet: 0.35 (0.31), residues: 259 loop : -1.00 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.008 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 0.02578 ( 150) hydrogen bonds : angle 5.00941 ( 408) SS BOND : bond 0.00313 ( 5) SS BOND : angle 0.69730 ( 10) covalent geometry : bond 0.00311 ( 4233) covalent geometry : angle 0.57372 ( 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 : 0.502 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.2554 time to fit residues: 17.4160 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 : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR 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: 2.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107435 restraints weight = 5684.157| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.17 r_work: 0.3219 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4238 Z= 0.218 Angle : 0.652 7.556 5773 Z= 0.333 Chirality : 0.047 0.154 653 Planarity : 0.005 0.063 735 Dihedral : 4.777 18.945 578 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.05 % Allowed : 12.45 % 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: -0.74 (0.36), residues: 533 helix: -3.63 (0.77), residues: 14 sheet: 0.25 (0.31), residues: 259 loop : -1.04 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 138 HIS 0.004 0.001 HIS H 71 PHE 0.009 0.002 PHE L 229 TYR 0.016 0.002 TYR L 70 ARG 0.005 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 150) hydrogen bonds : angle 5.38574 ( 408) SS BOND : bond 0.00388 ( 5) SS BOND : angle 0.89721 ( 10) covalent geometry : bond 0.00540 ( 4233) covalent geometry : angle 0.65199 ( 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 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.654 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.3757 time to fit residues: 23.7352 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 : 1.440 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.130391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113517 restraints weight = 5486.890| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4238 Z= 0.254 Angle : 0.689 8.025 5773 Z= 0.351 Chirality : 0.048 0.161 653 Planarity : 0.006 0.064 735 Dihedral : 4.980 19.457 578 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.84 % Allowed : 13.92 % Favored : 85.23 % 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: -0.85 (0.36), residues: 533 helix: -3.73 (0.77), residues: 13 sheet: 0.17 (0.31), residues: 260 loop : -1.12 (0.39), 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 0.010 0.002 PHE L 229 TYR 0.016 0.002 TYR L 70 ARG 0.005 0.001 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 150) hydrogen bonds : angle 5.55810 ( 408) SS BOND : bond 0.00422 ( 5) SS BOND : angle 0.98058 ( 10) covalent geometry : bond 0.00629 ( 4233) covalent geometry : angle 0.68863 ( 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 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.506 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.1583 time to fit residues: 9.7832 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 : 0.466 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 217 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.134375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117544 restraints weight = 5409.881| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.07 r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4238 Z= 0.144 Angle : 0.591 6.993 5773 Z= 0.300 Chirality : 0.045 0.154 653 Planarity : 0.005 0.063 735 Dihedral : 4.506 18.774 578 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.05 % Allowed : 14.35 % 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: -0.66 (0.36), residues: 533 helix: -3.64 (0.77), residues: 14 sheet: 0.28 (0.31), residues: 258 loop : -0.95 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS A 115 PHE 0.009 0.001 PHE A 139 TYR 0.010 0.001 TYR A 132 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 150) hydrogen bonds : angle 5.18904 ( 408) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.76363 ( 10) covalent geometry : bond 0.00352 ( 4233) covalent geometry : angle 0.59026 ( 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 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.500 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1590 time to fit residues: 10.6459 Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 33 VAL 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: 0.7980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.133318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116513 restraints weight = 5317.173| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.02 r_work: 0.3274 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1563 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= 0.136 Angle : 0.582 6.573 5773 Z= 0.295 Chirality : 0.045 0.162 653 Planarity : 0.005 0.063 735 Dihedral : 4.391 18.380 578 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.48 % Allowed : 14.35 % 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: -0.48 (0.37), residues: 533 helix: -3.53 (0.84), residues: 14 sheet: 0.43 (0.32), residues: 263 loop : -0.89 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS A 115 PHE 0.008 0.001 PHE A 139 TYR 0.010 0.001 TYR L 70 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 150) hydrogen bonds : angle 5.09665 ( 408) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.71927 ( 10) covalent geometry : bond 0.00335 ( 4233) covalent geometry : angle 0.58180 ( 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 55 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.483 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.1605 time to fit residues: 11.0635 Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 217 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.0470 chunk 19 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 115 HIS L 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119070 restraints weight = 5291.964| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.04 r_work: 0.3208 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4238 Z= 0.102 Angle : 0.546 6.403 5773 Z= 0.277 Chirality : 0.044 0.168 653 Planarity : 0.005 0.063 735 Dihedral : 4.093 17.363 578 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.05 % Allowed : 14.77 % 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: -0.31 (0.37), residues: 533 helix: -3.46 (0.91), residues: 14 sheet: 0.55 (0.32), residues: 258 loop : -0.76 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.006 0.001 HIS A 115 PHE 0.009 0.001 PHE A 139 TYR 0.007 0.001 TYR H 198 ARG 0.008 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02342 ( 150) hydrogen bonds : angle 4.84971 ( 408) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.63619 ( 10) covalent geometry : bond 0.00245 ( 4233) covalent geometry : angle 0.54630 ( 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 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.446 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1803 time to fit residues: 11.6865 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 : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116802 restraints weight = 5364.977| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.04 r_work: 0.3254 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4238 Z= 0.143 Angle : 0.583 6.494 5773 Z= 0.296 Chirality : 0.045 0.167 653 Planarity : 0.005 0.063 735 Dihedral : 4.305 17.622 578 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.05 % Allowed : 15.19 % Favored : 83.76 % 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: -0.28 (0.38), residues: 533 helix: -3.56 (0.83), residues: 14 sheet: 0.60 (0.32), residues: 263 loop : -0.80 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.006 0.001 HIS A 115 PHE 0.007 0.001 PHE A 139 TYR 0.011 0.001 TYR L 70 ARG 0.008 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 150) hydrogen bonds : angle 5.03196 ( 408) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.70172 ( 10) covalent geometry : bond 0.00351 ( 4233) covalent geometry : angle 0.58277 ( 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 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.454 Fit side-chains REVERT: H 233 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8026 (mm) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1664 time to fit residues: 10.6861 Evaluate side-chains 51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 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 233 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 217 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117291 restraints weight = 5353.566| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.01 r_work: 0.3269 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4238 Z= 0.133 Angle : 0.573 6.535 5773 Z= 0.290 Chirality : 0.044 0.162 653 Planarity : 0.005 0.062 735 Dihedral : 4.262 17.363 578 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.05 % Allowed : 15.19 % Favored : 83.76 % 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: -0.24 (0.38), residues: 533 helix: -3.54 (0.85), residues: 14 sheet: 0.63 (0.33), residues: 263 loop : -0.77 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.006 0.001 HIS A 115 PHE 0.008 0.001 PHE A 139 TYR 0.010 0.001 TYR L 70 ARG 0.008 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 150) hydrogen bonds : angle 4.99517 ( 408) SS BOND : bond 0.00332 ( 5) SS BOND : angle 0.68650 ( 10) covalent geometry : bond 0.00326 ( 4233) covalent geometry : angle 0.57307 ( 5763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.24 seconds wall clock time: 57 minutes 1.69 seconds (3421.69 seconds total)