Starting phenix.real_space_refine (version: dev) on Sun Dec 11 15:46:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/12_2022/7p2q_13172_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 4780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.10, per 1000 atoms: 0.65 Number of scatterers: 4780 At special positions: 0 Unit cell: (81.81, 84.24, 126.36, 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 23 16.00 O 873 8.00 N 778 7.00 C 3106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 624.7 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 41.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 removed outlier: 4.288A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.782A pdb=" N VAL A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 79 through 105 Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.516A pdb=" N GLU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.720A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.700A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.653A pdb=" N LEU D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 112 through 131 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.282A pdb=" N VAL A 110 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 126 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 112 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.094A pdb=" N VAL B 51 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 53 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 61 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.679A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.622A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 693 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: 1.18 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1460 1.34 - 1.46: 971 1.46 - 1.58: 2424 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4896 Sorted by residual: bond pdb=" C LEU D 131 " pdb=" N PRO D 132 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.88e+00 bond pdb=" C LYS C 111 " pdb=" N PRO C 112 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.53e+00 bond pdb=" CA LYS C 111 " pdb=" C LYS C 111 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 2.04e+00 bond pdb=" C GLU C 209 " pdb=" N PRO C 210 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.01e+00 bond pdb=" C PHE C 107 " pdb=" N PRO C 108 " ideal model delta sigma weight residual 1.337 1.351 -0.015 1.11e-02 8.12e+03 1.75e+00 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.41: 182 107.41 - 114.10: 2765 114.10 - 120.79: 2047 120.79 - 127.48: 1585 127.48 - 134.17: 50 Bond angle restraints: 6629 Sorted by residual: angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLU A 58 " pdb=" N SER A 59 " pdb=" CA SER A 59 " ideal model delta sigma weight residual 121.80 130.19 -8.39 2.44e+00 1.68e-01 1.18e+01 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.00e+01 angle pdb=" C2 NAG E 2 " pdb=" N2 NAG E 2 " pdb=" C7 NAG E 2 " ideal model delta sigma weight residual 123.12 127.18 -4.06 1.28e+00 6.08e-01 1.00e+01 ... (remaining 6624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.01: 2767 14.01 - 28.02: 105 28.02 - 42.03: 38 42.03 - 56.04: 0 56.04 - 70.05: 1 Dihedral angle restraints: 2911 sinusoidal: 1203 harmonic: 1708 Sorted by residual: dihedral pdb=" CA ASP C 154 " pdb=" C ASP C 154 " pdb=" N ASP C 155 " pdb=" CA ASP C 155 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR B 174 " pdb=" C TYR B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER D 74 " pdb=" C SER D 74 " pdb=" N LEU D 75 " pdb=" CA LEU D 75 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 530 0.045 - 0.091: 166 0.091 - 0.136: 51 0.136 - 0.182: 5 0.182 - 0.227: 4 Chirality restraints: 756 Sorted by residual: chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN B 134 " pdb=" N ASN B 134 " pdb=" C ASN B 134 " pdb=" CB ASN B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL B 103 " pdb=" CA VAL B 103 " pdb=" CG1 VAL B 103 " pdb=" CG2 VAL B 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 753 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 140 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 141 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 71 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 37 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.026 5.00e-02 4.00e+02 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1005 2.79 - 3.32: 4108 3.32 - 3.85: 7306 3.85 - 4.37: 7850 4.37 - 4.90: 13680 Nonbonded interactions: 33949 Sorted by model distance: nonbonded pdb=" NH1 ARG A 109 " pdb=" CE1 PHE B 86 " model vdw 2.264 3.420 nonbonded pdb=" O LYS B 121 " pdb=" OD1 ASP B 122 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG C 84 " pdb=" OE2 GLU C 136 " model vdw 2.352 2.520 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.357 2.440 nonbonded pdb=" OD1 ASP A 120 " pdb=" NZ LYS A 147 " model vdw 2.401 2.520 ... (remaining 33944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3106 2.51 5 N 778 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 1.990 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.050 Process input model: 16.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.003 0.041 4896 Z= 0.217 Angle : 0.802 9.532 6629 Z= 0.427 Chirality : 0.049 0.227 756 Planarity : 0.007 0.057 821 Dihedral : 8.692 70.055 1809 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.29), residues: 579 helix: -1.26 (0.24), residues: 220 sheet: -1.18 (0.47), residues: 120 loop : -3.26 (0.32), residues: 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2243 time to fit residues: 72.1393 Evaluate side-chains 146 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4896 Z= 0.247 Angle : 0.715 8.216 6629 Z= 0.368 Chirality : 0.044 0.204 756 Planarity : 0.006 0.080 821 Dihedral : 5.262 23.384 674 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.33), residues: 579 helix: 0.77 (0.32), residues: 220 sheet: -0.73 (0.49), residues: 126 loop : -2.72 (0.34), residues: 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1760 time to fit residues: 39.3455 Evaluate side-chains 128 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0450 time to fit residues: 0.8597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4896 Z= 0.170 Angle : 0.658 7.394 6629 Z= 0.331 Chirality : 0.043 0.150 756 Planarity : 0.005 0.050 821 Dihedral : 5.089 24.437 674 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.34), residues: 579 helix: 1.28 (0.33), residues: 225 sheet: -0.11 (0.49), residues: 127 loop : -2.76 (0.35), residues: 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1684 time to fit residues: 38.2298 Evaluate side-chains 142 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4896 Z= 0.184 Angle : 0.660 7.958 6629 Z= 0.330 Chirality : 0.042 0.171 756 Planarity : 0.004 0.045 821 Dihedral : 5.024 25.892 674 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.35), residues: 579 helix: 1.52 (0.34), residues: 225 sheet: -0.09 (0.49), residues: 129 loop : -2.50 (0.36), residues: 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1667 time to fit residues: 36.3095 Evaluate side-chains 135 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 0.0770 chunk 10 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 4896 Z= 0.162 Angle : 0.659 8.413 6629 Z= 0.326 Chirality : 0.043 0.196 756 Planarity : 0.004 0.040 821 Dihedral : 4.896 26.071 674 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.35), residues: 579 helix: 1.69 (0.34), residues: 226 sheet: 0.02 (0.50), residues: 129 loop : -2.40 (0.37), residues: 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1571 time to fit residues: 34.3868 Evaluate side-chains 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 143 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 4896 Z= 0.254 Angle : 0.705 8.422 6629 Z= 0.360 Chirality : 0.043 0.158 756 Planarity : 0.005 0.061 821 Dihedral : 5.142 29.208 674 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.36), residues: 579 helix: 1.58 (0.34), residues: 226 sheet: -0.08 (0.50), residues: 130 loop : -2.40 (0.37), residues: 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1568 time to fit residues: 31.8285 Evaluate side-chains 121 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 34 optimal weight: 0.0770 chunk 36 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4896 Z= 0.231 Angle : 0.681 8.536 6629 Z= 0.348 Chirality : 0.044 0.183 756 Planarity : 0.004 0.044 821 Dihedral : 5.214 29.668 674 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.36), residues: 579 helix: 1.69 (0.35), residues: 221 sheet: -0.08 (0.47), residues: 142 loop : -2.37 (0.38), residues: 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1754 time to fit residues: 34.7593 Evaluate side-chains 121 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4896 Z= 0.195 Angle : 0.685 8.732 6629 Z= 0.341 Chirality : 0.044 0.182 756 Planarity : 0.004 0.042 821 Dihedral : 5.196 29.837 674 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.35), residues: 579 helix: 1.59 (0.35), residues: 221 sheet: 0.03 (0.47), residues: 135 loop : -2.29 (0.38), residues: 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1636 time to fit residues: 34.1382 Evaluate side-chains 123 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 1.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 4896 Z= 0.169 Angle : 0.689 9.277 6629 Z= 0.341 Chirality : 0.045 0.178 756 Planarity : 0.004 0.044 821 Dihedral : 5.081 29.541 674 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.35), residues: 579 helix: 1.71 (0.35), residues: 221 sheet: 0.01 (0.48), residues: 129 loop : -2.25 (0.37), residues: 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1618 time to fit residues: 33.2847 Evaluate side-chains 126 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 4896 Z= 0.187 Angle : 0.695 9.386 6629 Z= 0.341 Chirality : 0.044 0.180 756 Planarity : 0.004 0.045 821 Dihedral : 5.024 29.617 674 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.35), residues: 579 helix: 1.58 (0.35), residues: 221 sheet: 0.00 (0.48), residues: 129 loop : -2.28 (0.37), residues: 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1572 time to fit residues: 31.6593 Evaluate side-chains 119 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 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 = 0.3594 r_free = 0.3594 target = 0.076257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060468 restraints weight = 28918.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061906 restraints weight = 22971.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063068 restraints weight = 19157.371| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4896 Z= 0.176 Angle : 0.700 9.441 6629 Z= 0.345 Chirality : 0.044 0.173 756 Planarity : 0.004 0.044 821 Dihedral : 4.973 29.458 674 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.35), residues: 579 helix: 1.58 (0.34), residues: 221 sheet: 0.21 (0.52), residues: 111 loop : -2.33 (0.35), residues: 247 =============================================================================== Job complete usr+sys time: 1367.07 seconds wall clock time: 25 minutes 21.73 seconds (1521.73 seconds total)