Starting phenix.real_space_refine on Tue Feb 11 04:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1b_33559/02_2025/7y1b_33559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1b_33559/02_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_33559/02_2025/7y1b_33559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1b_33559/02_2025/7y1b_33559.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1b_33559/02_2025/7y1b_33559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1b_33559/02_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-5592/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: 3.88, per 1000 atoms: 0.94 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: 1.19 Conformation dependent library (CDL) restraints added in 554.9 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: 0.53 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: 1.40 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- 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 4233 Z= 0.376 Angle : 0.636 6.244 5763 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 *********************** 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 : 0.488 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2003 time to fit residues: 13.0286 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 : 0.510 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 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 = 0.3551 r_free = 0.3551 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114855 restraints weight = 5462.030| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.11 r_work: 0.3254 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4233 Z= 0.227 Angle : 0.621 7.921 5763 Z= 0.317 Chirality : 0.046 0.161 653 Planarity : 0.005 0.064 735 Dihedral : 4.679 18.947 578 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.63 % Allowed : 5.49 % Favored : 93.88 % 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: -3.65 (0.96), residues: 13 sheet: 0.19 (0.31), residues: 261 loop : -1.29 (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 H 169 TYR 0.014 0.001 TYR A 132 ARG 0.006 0.001 ARG A 106 *********************** 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 : 0.479 Fit side-chains revert: symmetry clash REVERT: H 128 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8440 (mm-40) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1693 time to fit residues: 11.5341 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 : 0.495 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 0.0030 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111144 restraints weight = 5536.426| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.13 r_work: 0.3287 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4233 Z= 0.157 Angle : 0.556 6.275 5763 Z= 0.283 Chirality : 0.044 0.159 653 Planarity : 0.005 0.062 735 Dihedral : 4.230 18.139 578 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.63 % Allowed : 8.23 % Favored : 91.14 % 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 (0.36), residues: 533 helix: -3.56 (0.92), residues: 14 sheet: 0.28 (0.31), residues: 258 loop : -1.07 (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 0.008 0.001 PHE A 139 TYR 0.012 0.001 TYR A 132 ARG 0.006 0.000 ARG A 106 *********************** 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 51 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1726 time to fit residues: 11.2754 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 : 0.442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110025 restraints weight = 5562.405| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.15 r_work: 0.3286 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4233 Z= 0.198 Angle : 0.567 6.326 5763 Z= 0.288 Chirality : 0.044 0.160 653 Planarity : 0.005 0.061 735 Dihedral : 4.250 17.856 578 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.84 % Allowed : 10.34 % Favored : 88.82 % 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: -0.55 (0.37), residues: 533 helix: -3.53 (0.90), residues: 14 sheet: 0.40 (0.32), residues: 259 loop : -0.95 (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 0.007 0.001 PHE A 139 TYR 0.011 0.001 TYR L 70 ARG 0.004 0.000 ARG A 106 *********************** 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 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.1732 time to fit residues: 11.5718 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 : 0.487 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.128628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110839 restraints weight = 5605.377| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.18 r_work: 0.3270 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4233 Z= 0.227 Angle : 0.576 6.522 5763 Z= 0.292 Chirality : 0.044 0.153 653 Planarity : 0.005 0.062 735 Dihedral : 4.314 18.033 578 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.05 % Allowed : 11.39 % Favored : 87.55 % 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: -0.43 (0.37), residues: 533 helix: -3.55 (0.86), residues: 14 sheet: 0.51 (0.32), residues: 264 loop : -0.94 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 138 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.001 PHE A 139 TYR 0.012 0.001 TYR L 70 ARG 0.004 0.000 ARG A 106 *********************** 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 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.1631 time to fit residues: 11.1667 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 : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 197 THR 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: 0.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117414 restraints weight = 5412.825| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.02 r_work: 0.3271 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4233 Z= 0.246 Angle : 0.588 6.543 5763 Z= 0.298 Chirality : 0.045 0.158 653 Planarity : 0.005 0.062 735 Dihedral : 4.395 18.138 578 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -0.40 (0.37), residues: 533 helix: -3.61 (0.81), residues: 14 sheet: 0.49 (0.32), residues: 259 loop : -0.82 (0.41), 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 L 229 TYR 0.012 0.001 TYR L 70 ARG 0.005 0.001 ARG A 106 *********************** 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 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1683 time to fit residues: 11.1632 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 197 THR 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: 4.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113199 restraints weight = 5478.748| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.05 r_work: 0.3257 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4233 Z= 0.332 Angle : 0.638 7.074 5763 Z= 0.325 Chirality : 0.046 0.161 653 Planarity : 0.005 0.062 735 Dihedral : 4.665 18.607 578 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.05 % Allowed : 13.08 % Favored : 85.86 % 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: -0.50 (0.37), residues: 533 helix: -3.67 (0.76), residues: 14 sheet: 0.39 (0.32), residues: 259 loop : -0.84 (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 0.008 0.001 ARG A 106 *********************** 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 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.456 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1556 time to fit residues: 9.5693 Evaluate side-chains 46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 124 ASP 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: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119740 restraints weight = 5270.040| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.99 r_work: 0.3313 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4233 Z= 0.155 Angle : 0.548 6.106 5763 Z= 0.278 Chirality : 0.044 0.155 653 Planarity : 0.005 0.062 735 Dihedral : 4.176 17.748 578 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.05 % Allowed : 13.71 % 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: -0.22 (0.37), residues: 533 helix: -3.49 (0.89), residues: 14 sheet: 0.68 (0.33), residues: 258 loop : -0.77 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 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 *********************** 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 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.433 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1609 time to fit residues: 10.4045 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN 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 = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119094 restraints weight = 5298.665| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.02 r_work: 0.3307 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.003 0.032 4233 Z= 0.176 Angle : 0.549 6.031 5763 Z= 0.279 Chirality : 0.044 0.172 653 Planarity : 0.005 0.062 735 Dihedral : 4.129 17.380 578 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.63 % Allowed : 14.35 % Favored : 85.02 % 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: -0.09 (0.38), residues: 533 helix: -3.51 (0.88), residues: 14 sheet: 0.79 (0.33), residues: 263 loop : -0.74 (0.41), residues: 256 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 0.009 0.001 TYR L 70 ARG 0.007 0.000 ARG A 106 *********************** 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 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.475 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1729 time to fit residues: 10.1115 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 : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS 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: 0.8980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119379 restraints weight = 5325.757| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.01 r_work: 0.3241 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4233 Z= 0.182 Angle : 0.552 6.049 5763 Z= 0.280 Chirality : 0.044 0.168 653 Planarity : 0.005 0.059 735 Dihedral : 4.105 17.028 578 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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: -0.04 (0.38), residues: 533 helix: -3.50 (0.88), residues: 14 sheet: 0.83 (0.33), residues: 263 loop : -0.72 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 138 HIS 0.003 0.001 HIS H 71 PHE 0.008 0.001 PHE A 139 TYR 0.009 0.001 TYR L 70 ARG 0.008 0.000 ARG A 106 ********************** 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 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.518 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1748 time to fit residues: 10.2001 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS 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: 0.2980 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119673 restraints weight = 5313.565| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.04 r_work: 0.3284 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4233 Z= 0.174 Angle : 0.545 5.988 5763 Z= 0.276 Chirality : 0.043 0.168 653 Planarity : 0.005 0.059 735 Dihedral : 4.056 16.440 578 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.63 % Allowed : 14.98 % 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: 0.02 (0.38), residues: 533 helix: -3.51 (0.88), residues: 14 sheet: 0.88 (0.33), residues: 263 loop : -0.70 (0.41), residues: 256 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 0.008 0.000 ARG A 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.15 seconds wall clock time: 43 minutes 29.96 seconds (2609.96 seconds total)