Starting phenix.real_space_refine on Wed Jun 4 22:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.map" model { file = "/net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y97_10733/06_2025/6y97_10733.cif" } resolution = 4.33 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= 0.026 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 36 5.16 5 C 2840 2.51 5 N 700 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 3.73, per 1000 atoms: 0.85 Number of scatterers: 4366 At special positions: 0 Unit cell: (61.05, 65.934, 118.03, 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 36 16.00 O 790 8.00 N 700 7.00 C 2840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 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: 0.99 Conformation dependent library (CDL) restraints added in 506.9 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 50 through 70 removed outlier: 4.157A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.626A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.955A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 143 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 213 removed outlier: 4.121A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.880A pdb=" N SER B 49 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.855A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.301A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.521A pdb=" N LYS B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.617A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.510A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.177A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.646A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.056A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN L 50 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 42 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 609 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: 1.04 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1335 1.35 - 1.46: 1057 1.46 - 1.58: 2016 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 4468 Sorted by residual: bond pdb=" N GLN L 55 " pdb=" CA GLN L 55 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 bond pdb=" CB PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.23e+00 bond pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.07e-01 bond pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5971 2.11 - 4.21: 72 4.21 - 6.32: 8 6.32 - 8.43: 3 8.43 - 10.53: 1 Bond angle restraints: 6055 Sorted by residual: angle pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C GLN L 43 " pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 121.95 111.42 10.53 3.74e+00 7.15e-02 7.93e+00 angle pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " pdb=" CG GLN L 55 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.61e+00 angle pdb=" CA LYS B 50 " pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C GLN L 55 " pdb=" N MET L 56 " pdb=" CA MET L 56 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 6050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2369 17.99 - 35.98: 227 35.98 - 53.97: 46 53.97 - 71.96: 5 71.96 - 89.95: 5 Dihedral angle restraints: 2652 sinusoidal: 1031 harmonic: 1621 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 55.10 37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB MET A 93 " pdb=" CG MET A 93 " pdb=" SD MET A 93 " pdb=" CE MET A 93 " ideal model delta sinusoidal sigma weight residual -60.00 -113.09 53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CB MET A 136 " pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sinusoidal sigma weight residual 180.00 127.86 52.14 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 461 0.034 - 0.069: 154 0.069 - 0.103: 60 0.103 - 0.137: 12 0.137 - 0.172: 1 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE L 53 " pdb=" N ILE L 53 " pdb=" C ILE L 53 " pdb=" CB ILE L 53 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 685 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 78 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO B 79 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 63 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO L 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 9.89e-03 1.96e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 80 2.70 - 3.25: 4316 3.25 - 3.80: 6674 3.80 - 4.35: 7774 4.35 - 4.90: 13128 Nonbonded interactions: 31972 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OG SER H 30 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" O ALA A 126 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O ASN B 163 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR H 69 " pdb=" O GLU H 82 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASN A 171 " pdb=" OG SER A 173 " model vdw 2.271 3.040 ... (remaining 31967 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.930 Find NCS groups from input model: 0.090 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 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 : 0.002 0.055 4472 Z= 0.115 Angle : 0.578 10.533 6063 Z= 0.293 Chirality : 0.040 0.172 688 Planarity : 0.005 0.098 748 Dihedral : 14.610 89.950 1608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.38), residues: 556 helix: 2.81 (0.36), residues: 210 sheet: 0.41 (0.53), residues: 92 loop : -1.00 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS A 63 PHE 0.015 0.001 PHE B 146 TYR 0.024 0.001 TYR A 94 ARG 0.003 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.16067 ( 216) hydrogen bonds : angle 5.18148 ( 609) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.33322 ( 8) covalent geometry : bond 0.00240 ( 4468) covalent geometry : angle 0.57797 ( 6055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8963 (tmmt) REVERT: B 163 ASN cc_start: 0.6919 (t0) cc_final: 0.6613 (t0) REVERT: H 46 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7361 (tm-30) REVERT: H 48 MET cc_start: 0.6951 (ppp) cc_final: 0.6250 (ppp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1301 time to fit residues: 27.3783 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0270 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 181 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.145931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123896 restraints weight = 11552.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.127738 restraints weight = 7696.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130687 restraints weight = 5479.853| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4472 Z= 0.129 Angle : 0.569 6.882 6063 Z= 0.288 Chirality : 0.041 0.138 688 Planarity : 0.005 0.061 748 Dihedral : 3.720 14.480 603 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.21 % Allowed : 4.99 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.38), residues: 556 helix: 2.59 (0.35), residues: 226 sheet: 0.65 (0.54), residues: 89 loop : -1.02 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 89 HIS 0.002 0.001 HIS B 63 PHE 0.028 0.002 PHE A 62 TYR 0.022 0.001 TYR A 94 ARG 0.002 0.000 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 216) hydrogen bonds : angle 4.00956 ( 609) SS BOND : bond 0.00402 ( 4) SS BOND : angle 1.26731 ( 8) covalent geometry : bond 0.00289 ( 4468) covalent geometry : angle 0.56775 ( 6055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8568 (pp) cc_final: 0.8153 (tt) REVERT: A 187 GLN cc_start: 0.8764 (mt0) cc_final: 0.8460 (mt0) REVERT: B 50 LYS cc_start: 0.9291 (tmtt) cc_final: 0.8999 (tmmt) REVERT: B 163 ASN cc_start: 0.7958 (t0) cc_final: 0.7737 (t0) REVERT: H 13 LYS cc_start: 0.7275 (tppt) cc_final: 0.7046 (mmmt) REVERT: H 27 TYR cc_start: 0.8504 (p90) cc_final: 0.8155 (p90) REVERT: H 46 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7893 (tm-30) REVERT: H 47 TRP cc_start: 0.9046 (t60) cc_final: 0.8284 (t60) REVERT: H 48 MET cc_start: 0.8274 (ppp) cc_final: 0.7612 (ppp) REVERT: H 57 ASP cc_start: 0.9061 (t0) cc_final: 0.8825 (t0) REVERT: H 81 MET cc_start: 0.3534 (tpt) cc_final: 0.3280 (tpt) REVERT: H 90 ASP cc_start: 0.8642 (m-30) cc_final: 0.8330 (m-30) REVERT: L 6 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6284 (mp10) REVERT: L 42 LEU cc_start: 0.8942 (mm) cc_final: 0.8482 (mm) REVERT: L 107 THR cc_start: 0.7814 (p) cc_final: 0.7572 (p) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1313 time to fit residues: 26.7824 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0060 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.145055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.123680 restraints weight = 11197.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127606 restraints weight = 7338.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130439 restraints weight = 5159.893| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4472 Z= 0.113 Angle : 0.571 6.695 6063 Z= 0.283 Chirality : 0.041 0.136 688 Planarity : 0.005 0.053 748 Dihedral : 3.757 13.704 603 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.38), residues: 556 helix: 2.75 (0.34), residues: 225 sheet: 0.54 (0.52), residues: 98 loop : -1.15 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 89 HIS 0.003 0.001 HIS A 63 PHE 0.017 0.001 PHE A 62 TYR 0.023 0.001 TYR A 94 ARG 0.004 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 216) hydrogen bonds : angle 3.77452 ( 609) SS BOND : bond 0.00890 ( 4) SS BOND : angle 1.04455 ( 8) covalent geometry : bond 0.00253 ( 4468) covalent geometry : angle 0.57023 ( 6055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8656 (pp) cc_final: 0.8229 (tt) REVERT: A 183 CYS cc_start: 0.7573 (p) cc_final: 0.7343 (p) REVERT: A 187 GLN cc_start: 0.8708 (mt0) cc_final: 0.8447 (mt0) REVERT: B 50 LYS cc_start: 0.9240 (tmtt) cc_final: 0.8981 (tmmt) REVERT: B 59 ASN cc_start: 0.8098 (m110) cc_final: 0.7799 (m-40) REVERT: B 71 MET cc_start: 0.5340 (ptp) cc_final: 0.5003 (ptp) REVERT: H 13 LYS cc_start: 0.7188 (tppt) cc_final: 0.6908 (mmmt) REVERT: H 27 TYR cc_start: 0.8548 (p90) cc_final: 0.8050 (p90) REVERT: H 46 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7940 (tm-30) REVERT: H 47 TRP cc_start: 0.8989 (t60) cc_final: 0.8108 (t60) REVERT: H 48 MET cc_start: 0.8148 (ppp) cc_final: 0.7349 (ppp) REVERT: H 90 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: L 42 LEU cc_start: 0.9036 (mm) cc_final: 0.8515 (mm) REVERT: L 107 THR cc_start: 0.7996 (p) cc_final: 0.7615 (p) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1246 time to fit residues: 24.9825 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 158 HIS ** L 95 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109495 restraints weight = 11732.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113246 restraints weight = 7521.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116078 restraints weight = 5218.958| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4472 Z= 0.195 Angle : 0.652 6.370 6063 Z= 0.344 Chirality : 0.043 0.141 688 Planarity : 0.005 0.050 748 Dihedral : 4.587 19.648 603 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.37), residues: 556 helix: 2.36 (0.34), residues: 226 sheet: 0.79 (0.52), residues: 88 loop : -1.36 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 89 HIS 0.003 0.001 HIS B 63 PHE 0.019 0.003 PHE B 146 TYR 0.027 0.002 TYR A 94 ARG 0.008 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 216) hydrogen bonds : angle 4.01582 ( 609) SS BOND : bond 0.01367 ( 4) SS BOND : angle 1.30918 ( 8) covalent geometry : bond 0.00409 ( 4468) covalent geometry : angle 0.65043 ( 6055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8829 (pp) cc_final: 0.8394 (tt) REVERT: A 166 ASN cc_start: 0.8818 (t0) cc_final: 0.8550 (t0) REVERT: A 174 GLU cc_start: 0.9249 (mp0) cc_final: 0.8890 (mp0) REVERT: A 205 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 50 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9091 (tmmt) REVERT: H 13 LYS cc_start: 0.7326 (tppt) cc_final: 0.7012 (mmmt) REVERT: H 47 TRP cc_start: 0.9035 (t60) cc_final: 0.8424 (t60) REVERT: H 48 MET cc_start: 0.8216 (ppp) cc_final: 0.7404 (ppp) REVERT: H 57 ASP cc_start: 0.8999 (t70) cc_final: 0.8631 (t0) REVERT: H 81 MET cc_start: 0.4095 (tpt) cc_final: 0.3794 (tpt) REVERT: H 90 ASP cc_start: 0.8942 (m-30) cc_final: 0.8666 (m-30) REVERT: H 102 ASP cc_start: 0.8377 (t0) cc_final: 0.8134 (t0) REVERT: L 42 LEU cc_start: 0.9171 (mm) cc_final: 0.8938 (mm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1385 time to fit residues: 26.9818 Evaluate side-chains 126 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.0000 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 140 ASN B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.134294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113685 restraints weight = 11783.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117650 restraints weight = 7534.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.120513 restraints weight = 5193.406| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4472 Z= 0.120 Angle : 0.624 6.622 6063 Z= 0.310 Chirality : 0.042 0.132 688 Planarity : 0.005 0.043 748 Dihedral : 4.310 16.766 603 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.38), residues: 556 helix: 2.50 (0.34), residues: 225 sheet: 0.89 (0.53), residues: 88 loop : -1.28 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.001 0.000 HIS B 63 PHE 0.017 0.002 PHE L 67 TYR 0.030 0.002 TYR A 94 ARG 0.003 0.001 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 216) hydrogen bonds : angle 3.78852 ( 609) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.12087 ( 8) covalent geometry : bond 0.00272 ( 4468) covalent geometry : angle 0.62267 ( 6055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8969 (m110) cc_final: 0.8748 (m110) REVERT: A 133 LEU cc_start: 0.8892 (pp) cc_final: 0.8498 (tt) REVERT: A 166 ASN cc_start: 0.8596 (t0) cc_final: 0.7891 (m-40) REVERT: A 174 GLU cc_start: 0.9110 (mp0) cc_final: 0.8669 (mp0) REVERT: A 183 CYS cc_start: 0.7684 (p) cc_final: 0.7414 (p) REVERT: A 205 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 50 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9073 (tmmt) REVERT: H 13 LYS cc_start: 0.7322 (tppt) cc_final: 0.6977 (mmmt) REVERT: H 19 LYS cc_start: 0.8823 (mppt) cc_final: 0.8618 (mmtm) REVERT: H 46 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7514 (tm-30) REVERT: H 47 TRP cc_start: 0.8964 (t60) cc_final: 0.8427 (t60) REVERT: H 48 MET cc_start: 0.8225 (ppp) cc_final: 0.7538 (ppp) REVERT: H 57 ASP cc_start: 0.8970 (t70) cc_final: 0.8592 (t0) REVERT: H 90 ASP cc_start: 0.8951 (m-30) cc_final: 0.8679 (m-30) REVERT: H 102 ASP cc_start: 0.8414 (t0) cc_final: 0.8105 (t0) REVERT: L 4 MET cc_start: 0.8718 (mpp) cc_final: 0.8382 (mpp) REVERT: L 42 LEU cc_start: 0.9368 (mm) cc_final: 0.9150 (mm) REVERT: L 102 THR cc_start: 0.8096 (m) cc_final: 0.7834 (m) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1341 time to fit residues: 27.5847 Evaluate side-chains 134 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.0270 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.125731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106219 restraints weight = 11945.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109900 restraints weight = 7643.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112510 restraints weight = 5275.275| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4472 Z= 0.174 Angle : 0.674 7.344 6063 Z= 0.345 Chirality : 0.043 0.142 688 Planarity : 0.005 0.047 748 Dihedral : 4.723 19.811 603 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.37), residues: 556 helix: 2.26 (0.34), residues: 223 sheet: 0.64 (0.53), residues: 88 loop : -1.38 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 33 HIS 0.003 0.001 HIS L 31 PHE 0.022 0.003 PHE A 200 TYR 0.029 0.002 TYR A 94 ARG 0.006 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 216) hydrogen bonds : angle 4.14828 ( 609) SS BOND : bond 0.00801 ( 4) SS BOND : angle 1.32384 ( 8) covalent geometry : bond 0.00386 ( 4468) covalent geometry : angle 0.67318 ( 6055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9045 (mmt) cc_final: 0.8830 (mmt) REVERT: A 133 LEU cc_start: 0.8976 (pp) cc_final: 0.8741 (mm) REVERT: A 171 ASN cc_start: 0.8952 (p0) cc_final: 0.8154 (p0) REVERT: A 174 GLU cc_start: 0.9199 (mp0) cc_final: 0.8778 (mp0) REVERT: A 187 GLN cc_start: 0.8738 (mt0) cc_final: 0.8471 (mt0) REVERT: A 205 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8571 (tm-30) REVERT: B 50 LYS cc_start: 0.9437 (tmtt) cc_final: 0.9144 (tmmt) REVERT: B 59 ASN cc_start: 0.8469 (m110) cc_final: 0.8190 (m110) REVERT: B 148 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8276 (pttt) REVERT: B 165 TYR cc_start: 0.8090 (m-80) cc_final: 0.7882 (m-10) REVERT: H 19 LYS cc_start: 0.9030 (mppt) cc_final: 0.8754 (mmtm) REVERT: H 46 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7526 (tm-30) REVERT: H 47 TRP cc_start: 0.8975 (t60) cc_final: 0.8457 (t60) REVERT: H 48 MET cc_start: 0.8342 (ppp) cc_final: 0.7610 (ppp) REVERT: H 57 ASP cc_start: 0.8922 (t70) cc_final: 0.8679 (t0) REVERT: H 81 MET cc_start: 0.4291 (tpt) cc_final: 0.4045 (tpt) REVERT: H 90 ASP cc_start: 0.8999 (m-30) cc_final: 0.8717 (m-30) REVERT: H 102 ASP cc_start: 0.8413 (t0) cc_final: 0.8161 (t0) REVERT: L 4 MET cc_start: 0.8654 (mpp) cc_final: 0.8349 (mpp) REVERT: L 42 LEU cc_start: 0.9378 (mm) cc_final: 0.9147 (mm) REVERT: L 50 GLN cc_start: 0.8382 (pm20) cc_final: 0.8119 (pm20) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1210 time to fit residues: 24.0533 Evaluate side-chains 133 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.128633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108810 restraints weight = 11629.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.112600 restraints weight = 7334.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.115393 restraints weight = 5023.759| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4472 Z= 0.136 Angle : 0.659 7.331 6063 Z= 0.333 Chirality : 0.043 0.141 688 Planarity : 0.005 0.046 748 Dihedral : 4.642 18.806 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.37), residues: 556 helix: 2.23 (0.35), residues: 223 sheet: 0.66 (0.52), residues: 88 loop : -1.38 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.025 0.002 PHE A 62 TYR 0.032 0.002 TYR A 94 ARG 0.004 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 216) hydrogen bonds : angle 3.95198 ( 609) SS BOND : bond 0.00231 ( 4) SS BOND : angle 1.12327 ( 8) covalent geometry : bond 0.00310 ( 4468) covalent geometry : angle 0.65846 ( 6055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.9061 (m110) cc_final: 0.8839 (m110) REVERT: A 133 LEU cc_start: 0.8967 (pp) cc_final: 0.8761 (mm) REVERT: A 166 ASN cc_start: 0.8792 (t0) cc_final: 0.8090 (m-40) REVERT: A 171 ASN cc_start: 0.8791 (p0) cc_final: 0.8014 (p0) REVERT: A 174 GLU cc_start: 0.9163 (mp0) cc_final: 0.8820 (mp0) REVERT: A 187 GLN cc_start: 0.8684 (mt0) cc_final: 0.8406 (mt0) REVERT: A 205 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 50 LYS cc_start: 0.9437 (tmtt) cc_final: 0.9156 (tmmt) REVERT: B 59 ASN cc_start: 0.8300 (m110) cc_final: 0.7982 (m110) REVERT: B 148 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8171 (pttt) REVERT: H 19 LYS cc_start: 0.8989 (mppt) cc_final: 0.8696 (mmtm) REVERT: H 46 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7462 (tm-30) REVERT: H 47 TRP cc_start: 0.8964 (t60) cc_final: 0.8432 (t60) REVERT: H 48 MET cc_start: 0.8285 (ppp) cc_final: 0.7638 (ppp) REVERT: H 57 ASP cc_start: 0.8891 (t70) cc_final: 0.8649 (t0) REVERT: H 81 MET cc_start: 0.4155 (tpt) cc_final: 0.3933 (tpt) REVERT: H 90 ASP cc_start: 0.9033 (m-30) cc_final: 0.8724 (m-30) REVERT: H 102 ASP cc_start: 0.8458 (t0) cc_final: 0.8181 (t0) REVERT: L 102 THR cc_start: 0.8222 (m) cc_final: 0.7911 (m) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1330 time to fit residues: 26.4770 Evaluate side-chains 131 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS B 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.128928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109516 restraints weight = 11904.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113170 restraints weight = 7579.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.115835 restraints weight = 5251.138| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4472 Z= 0.131 Angle : 0.657 8.371 6063 Z= 0.329 Chirality : 0.043 0.150 688 Planarity : 0.005 0.049 748 Dihedral : 4.606 17.351 603 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.37), residues: 556 helix: 2.28 (0.34), residues: 223 sheet: 0.60 (0.52), residues: 88 loop : -1.37 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 33 HIS 0.008 0.001 HIS B 145 PHE 0.036 0.002 PHE A 62 TYR 0.031 0.002 TYR A 94 ARG 0.006 0.001 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 216) hydrogen bonds : angle 3.89369 ( 609) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.04288 ( 8) covalent geometry : bond 0.00297 ( 4468) covalent geometry : angle 0.65669 ( 6055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8976 (m110) cc_final: 0.8726 (m110) REVERT: A 166 ASN cc_start: 0.8773 (t0) cc_final: 0.8094 (m-40) REVERT: A 171 ASN cc_start: 0.8768 (p0) cc_final: 0.8042 (p0) REVERT: A 174 GLU cc_start: 0.9192 (mp0) cc_final: 0.8855 (mp0) REVERT: A 205 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 50 LYS cc_start: 0.9448 (tmtt) cc_final: 0.9122 (tmmt) REVERT: B 148 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8262 (pttt) REVERT: H 19 LYS cc_start: 0.9001 (mppt) cc_final: 0.8706 (mmtm) REVERT: H 46 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 47 TRP cc_start: 0.8969 (t60) cc_final: 0.8404 (t60) REVERT: H 48 MET cc_start: 0.8157 (ppp) cc_final: 0.7604 (ppp) REVERT: H 57 ASP cc_start: 0.8876 (t70) cc_final: 0.8639 (t0) REVERT: H 81 MET cc_start: 0.4199 (tpt) cc_final: 0.3917 (tpt) REVERT: H 102 ASP cc_start: 0.8447 (t0) cc_final: 0.8139 (t0) REVERT: L 102 THR cc_start: 0.8109 (m) cc_final: 0.7754 (m) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1319 time to fit residues: 27.1499 Evaluate side-chains 136 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107866 restraints weight = 11853.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111611 restraints weight = 7488.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.114303 restraints weight = 5120.893| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4472 Z= 0.135 Angle : 0.666 8.428 6063 Z= 0.332 Chirality : 0.043 0.162 688 Planarity : 0.005 0.056 748 Dihedral : 4.614 18.012 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.37), residues: 556 helix: 2.32 (0.35), residues: 223 sheet: 0.49 (0.51), residues: 98 loop : -1.45 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 105 HIS 0.013 0.002 HIS B 145 PHE 0.028 0.002 PHE A 62 TYR 0.031 0.002 TYR A 94 ARG 0.003 0.000 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 216) hydrogen bonds : angle 3.91614 ( 609) SS BOND : bond 0.00313 ( 4) SS BOND : angle 1.01709 ( 8) covalent geometry : bond 0.00306 ( 4468) covalent geometry : angle 0.66507 ( 6055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASN cc_start: 0.8784 (t0) cc_final: 0.8210 (m110) REVERT: A 171 ASN cc_start: 0.8738 (p0) cc_final: 0.8054 (p0) REVERT: A 174 GLU cc_start: 0.9278 (mp0) cc_final: 0.8873 (mp0) REVERT: A 187 GLN cc_start: 0.8808 (mt0) cc_final: 0.8433 (mt0) REVERT: A 205 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 50 LYS cc_start: 0.9472 (tmtt) cc_final: 0.9168 (tmmt) REVERT: B 59 ASN cc_start: 0.8726 (m110) cc_final: 0.8496 (m110) REVERT: B 148 LYS cc_start: 0.8611 (mmtm) cc_final: 0.8243 (pttt) REVERT: H 19 LYS cc_start: 0.9057 (mppt) cc_final: 0.8758 (mmtm) REVERT: H 39 GLN cc_start: 0.7770 (tp40) cc_final: 0.7537 (tp40) REVERT: H 46 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7436 (tm-30) REVERT: H 47 TRP cc_start: 0.8963 (t60) cc_final: 0.8414 (t60) REVERT: H 48 MET cc_start: 0.8181 (ppp) cc_final: 0.7699 (ppp) REVERT: H 57 ASP cc_start: 0.8882 (t70) cc_final: 0.8667 (t0) REVERT: H 81 MET cc_start: 0.4238 (tpt) cc_final: 0.3966 (tpt) REVERT: H 102 ASP cc_start: 0.8483 (t0) cc_final: 0.8174 (t0) REVERT: L 102 THR cc_start: 0.8090 (m) cc_final: 0.7722 (m) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1393 time to fit residues: 29.4514 Evaluate side-chains 140 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN B 56 GLN B 140 ASN B 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.127643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108478 restraints weight = 11501.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.112087 restraints weight = 7246.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114687 restraints weight = 4988.193| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4472 Z= 0.128 Angle : 0.674 9.266 6063 Z= 0.335 Chirality : 0.044 0.167 688 Planarity : 0.005 0.055 748 Dihedral : 4.566 16.636 603 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.37), residues: 556 helix: 2.27 (0.35), residues: 223 sheet: 0.40 (0.51), residues: 98 loop : -1.49 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 105 HIS 0.010 0.002 HIS B 145 PHE 0.041 0.002 PHE B 62 TYR 0.031 0.002 TYR A 94 ARG 0.002 0.000 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 216) hydrogen bonds : angle 3.89811 ( 609) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.92121 ( 8) covalent geometry : bond 0.00290 ( 4468) covalent geometry : angle 0.67322 ( 6055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8784 (t80) cc_final: 0.8032 (t80) REVERT: A 166 ASN cc_start: 0.8807 (t0) cc_final: 0.8272 (m110) REVERT: A 171 ASN cc_start: 0.8731 (p0) cc_final: 0.8088 (p0) REVERT: A 174 GLU cc_start: 0.9235 (mp0) cc_final: 0.8931 (mp0) REVERT: A 187 GLN cc_start: 0.8795 (mt0) cc_final: 0.8427 (mt0) REVERT: A 205 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 50 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9110 (tmmt) REVERT: B 137 ASP cc_start: 0.8342 (t0) cc_final: 0.8118 (t0) REVERT: B 148 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8263 (pttt) REVERT: H 19 LYS cc_start: 0.9045 (mppt) cc_final: 0.8708 (mmtm) REVERT: H 46 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7474 (tm-30) REVERT: H 47 TRP cc_start: 0.8965 (t60) cc_final: 0.8403 (t60) REVERT: H 48 MET cc_start: 0.8282 (ppp) cc_final: 0.7714 (ppp) REVERT: H 57 ASP cc_start: 0.8961 (t70) cc_final: 0.8623 (t0) REVERT: H 81 MET cc_start: 0.4224 (tpt) cc_final: 0.3967 (tpt) REVERT: H 102 ASP cc_start: 0.8487 (t0) cc_final: 0.8159 (t0) REVERT: H 106 LEU cc_start: 0.9235 (tt) cc_final: 0.8979 (tt) REVERT: L 102 THR cc_start: 0.8048 (m) cc_final: 0.7618 (m) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1385 time to fit residues: 29.1779 Evaluate side-chains 139 residues out of total 481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.125054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105534 restraints weight = 12099.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109299 restraints weight = 7487.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111921 restraints weight = 5076.496| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4472 Z= 0.143 Angle : 0.680 8.766 6063 Z= 0.339 Chirality : 0.044 0.166 688 Planarity : 0.005 0.052 748 Dihedral : 4.654 17.872 603 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.38), residues: 556 helix: 2.28 (0.35), residues: 223 sheet: 0.36 (0.52), residues: 98 loop : -1.47 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.011 0.002 HIS B 145 PHE 0.033 0.003 PHE A 62 TYR 0.032 0.002 TYR A 94 ARG 0.004 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 216) hydrogen bonds : angle 3.97434 ( 609) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.99665 ( 8) covalent geometry : bond 0.00321 ( 4468) covalent geometry : angle 0.67929 ( 6055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.94 seconds wall clock time: 31 minutes 39.29 seconds (1899.29 seconds total)