Starting phenix.real_space_refine on Sat Apr 26 17:22:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw6_39624/04_2025/8yw6_39624.cif" } resolution = 3.18 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'PC8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 3.36, per 1000 atoms: 1.22 Number of scatterers: 2747 At special positions: 0 Unit cell: (78.66, 79.23, 91.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 335.7 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 61.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.708A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 125 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.585A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 489 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: 0.78 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 777 1.43 - 1.56: 1581 1.56 - 1.68: 19 1.68 - 1.81: 28 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.10e-02 8.26e+03 8.47e+01 bond pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.433 -0.099 1.10e-02 8.26e+03 8.17e+01 bond pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.23e+01 bond pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.06e+01 bond pdb=" OB2 CDL B 202 " pdb=" PB2 CDL B 202 " ideal model delta sigma weight residual 1.579 1.669 -0.090 1.50e-02 4.44e+03 3.62e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 3727 3.23 - 6.46: 51 6.46 - 9.69: 7 9.69 - 12.93: 1 12.93 - 16.16: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 202 " pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 111.33 118.92 -7.59 1.32e+00 5.72e-01 3.30e+01 angle pdb=" O3 PC8 B 201 " pdb=" P1 PC8 B 201 " pdb=" O4 PC8 B 201 " ideal model delta sigma weight residual 93.28 109.44 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C31 CDL B 202 " pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.39 -8.75 1.65e+00 3.69e-01 2.83e+01 angle pdb=" C71 CDL B 202 " pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.11 -8.47 1.65e+00 3.69e-01 2.65e+01 angle pdb=" C11 CDL B 202 " pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 111.33 117.31 -5.98 1.32e+00 5.72e-01 2.05e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 1619 32.93 - 65.85: 70 65.85 - 98.78: 3 98.78 - 131.71: 0 131.71 - 164.63: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" O5 PC8 B 201 " pdb=" C7 PC8 B 201 " pdb=" C8 PC8 B 201 " pdb=" O7 PC8 B 201 " ideal model delta sinusoidal sigma weight residual 52.89 -142.48 -164.63 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA5 CDL B 202 " pdb=" CA4 CDL B 202 " pdb=" OA6 CDL B 202 " pdb=" CA6 CDL B 202 " ideal model delta sinusoidal sigma weight residual 168.24 75.71 92.53 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CA TYR C 35 " pdb=" C TYR C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 285 0.052 - 0.104: 70 0.104 - 0.155: 26 0.155 - 0.207: 7 0.207 - 0.259: 4 Chirality restraints: 392 Sorted by residual: chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN A 77 " pdb=" N ASN A 77 " pdb=" C ASN A 77 " pdb=" CB ASN A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ARG B 62 " pdb=" N ARG B 62 " pdb=" C ARG B 62 " pdb=" CB ARG B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 76 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG A 76 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG A 76 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 77 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 25 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 53 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C SER C 53 " -0.024 2.00e-02 2.50e+03 pdb=" O SER C 53 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1003 2.90 - 3.40: 2614 3.40 - 3.90: 4765 3.90 - 4.40: 5264 4.40 - 4.90: 8613 Nonbonded interactions: 22259 Sorted by model distance: nonbonded pdb=" OD2 ASP C 73 " pdb=" NZ LYS C 76 " model vdw 2.395 3.120 nonbonded pdb=" O4 PC8 B 201 " pdb=" O7 PC8 B 201 " model vdw 2.468 2.432 nonbonded pdb=" O GLU C 31 " pdb=" OG SER C 53 " model vdw 2.547 3.040 nonbonded pdb=" OD1 ASP B 18 " pdb=" NH2 ARG B 39 " model vdw 2.555 3.120 nonbonded pdb=" C1 PC8 B 201 " pdb=" C3 PC8 B 201 " model vdw 2.609 3.088 ... (remaining 22254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.012 0.105 2815 Z= 0.693 Angle : 1.003 16.157 3789 Z= 0.596 Chirality : 0.061 0.259 392 Planarity : 0.004 0.042 464 Dihedral : 16.353 164.632 1076 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 1.48 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.94 (0.47), residues: 327 helix: 0.65 (0.36), residues: 176 sheet: -0.31 (0.70), residues: 55 loop : 1.64 (0.73), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 102 HIS 0.001 0.000 HIS A 26 PHE 0.001 0.000 PHE A 66 TYR 0.008 0.000 TYR C 95 ARG 0.001 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.16961 ( 175) hydrogen bonds : angle 6.83407 ( 489) SS BOND : bond 0.01024 ( 1) SS BOND : angle 0.98399 ( 2) covalent geometry : bond 0.01172 ( 2814) covalent geometry : angle 1.00332 ( 3787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.303 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.3085 time to fit residues: 11.2707 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.187821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131381 restraints weight = 2802.136| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.39 r_work: 0.3256 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2815 Z= 0.130 Angle : 0.490 5.586 3789 Z= 0.260 Chirality : 0.041 0.133 392 Planarity : 0.004 0.037 464 Dihedral : 17.071 171.517 476 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.64 (0.46), residues: 327 helix: 2.38 (0.38), residues: 177 sheet: 0.10 (0.69), residues: 49 loop : 1.72 (0.65), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.015 0.001 TYR C 95 ARG 0.008 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 175) hydrogen bonds : angle 4.37472 ( 489) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.75453 ( 2) covalent geometry : bond 0.00299 ( 2814) covalent geometry : angle 0.49018 ( 3787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.273 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.2007 time to fit residues: 4.9394 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.182764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127238 restraints weight = 2787.350| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.31 r_work: 0.3215 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2815 Z= 0.143 Angle : 0.480 6.029 3789 Z= 0.252 Chirality : 0.042 0.141 392 Planarity : 0.004 0.035 464 Dihedral : 15.115 149.122 476 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 4.81 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.63 (0.47), residues: 327 helix: 2.47 (0.39), residues: 179 sheet: 0.03 (0.68), residues: 51 loop : 1.55 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.002 PHE A 69 TYR 0.015 0.002 TYR C 95 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 175) hydrogen bonds : angle 4.08568 ( 489) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.76275 ( 2) covalent geometry : bond 0.00343 ( 2814) covalent geometry : angle 0.47942 ( 3787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.237 Fit side-chains REVERT: C 32 ARG cc_start: 0.7751 (mmp80) cc_final: 0.7497 (mmp80) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.1897 time to fit residues: 6.3776 Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.186729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131438 restraints weight = 2828.184| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.34 r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2815 Z= 0.091 Angle : 0.416 5.198 3789 Z= 0.219 Chirality : 0.038 0.129 392 Planarity : 0.004 0.034 464 Dihedral : 14.029 144.762 476 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 6.67 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.05 (0.46), residues: 327 helix: 2.95 (0.39), residues: 174 sheet: 0.18 (0.68), residues: 50 loop : 1.53 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.003 0.000 HIS A 84 PHE 0.009 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 175) hydrogen bonds : angle 3.75209 ( 489) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.72101 ( 2) covalent geometry : bond 0.00198 ( 2814) covalent geometry : angle 0.41602 ( 3787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.277 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2067 time to fit residues: 5.7751 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.180890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124762 restraints weight = 2827.752| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.37 r_work: 0.3190 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2815 Z= 0.152 Angle : 0.474 5.890 3789 Z= 0.249 Chirality : 0.042 0.140 392 Planarity : 0.004 0.034 464 Dihedral : 14.004 142.533 476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.84 (0.46), residues: 327 helix: 2.72 (0.39), residues: 174 sheet: 0.12 (0.67), residues: 50 loop : 1.53 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.005 0.001 HIS A 84 PHE 0.016 0.002 PHE A 69 TYR 0.016 0.002 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 175) hydrogen bonds : angle 3.93860 ( 489) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.64660 ( 2) covalent geometry : bond 0.00370 ( 2814) covalent geometry : angle 0.47367 ( 3787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.313 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2147 time to fit residues: 6.2142 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 28 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.185721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130583 restraints weight = 2809.238| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.35 r_work: 0.3261 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2815 Z= 0.094 Angle : 0.411 5.138 3789 Z= 0.215 Chirality : 0.038 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 13.053 138.629 476 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.99 (0.46), residues: 327 helix: 2.85 (0.39), residues: 175 sheet: 0.20 (0.67), residues: 50 loop : 1.54 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.003 0.000 HIS A 84 PHE 0.009 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 175) hydrogen bonds : angle 3.64397 ( 489) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.62105 ( 2) covalent geometry : bond 0.00211 ( 2814) covalent geometry : angle 0.41045 ( 3787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1869 time to fit residues: 5.6736 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128571 restraints weight = 2884.744| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.37 r_work: 0.3236 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2815 Z= 0.106 Angle : 0.425 5.227 3789 Z= 0.222 Chirality : 0.039 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 12.560 136.265 476 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.02 (0.46), residues: 327 helix: 2.84 (0.39), residues: 175 sheet: 0.30 (0.67), residues: 50 loop : 1.57 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 175) hydrogen bonds : angle 3.65102 ( 489) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.49940 ( 2) covalent geometry : bond 0.00248 ( 2814) covalent geometry : angle 0.42473 ( 3787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.279 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1451 time to fit residues: 4.1149 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.182531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128145 restraints weight = 2837.434| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.33 r_work: 0.3228 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.114 Angle : 0.428 5.341 3789 Z= 0.224 Chirality : 0.039 0.127 392 Planarity : 0.004 0.033 464 Dihedral : 12.516 136.395 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 10.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.00 (0.47), residues: 327 helix: 2.81 (0.39), residues: 174 sheet: 0.35 (0.68), residues: 50 loop : 1.58 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 175) hydrogen bonds : angle 3.68635 ( 489) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.72308 ( 2) covalent geometry : bond 0.00267 ( 2814) covalent geometry : angle 0.42821 ( 3787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.302 Fit side-chains REVERT: B 39 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8183 (mtp85) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.2078 time to fit residues: 5.8188 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.180396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124426 restraints weight = 2831.975| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.37 r_work: 0.3176 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.132 Angle : 0.451 5.527 3789 Z= 0.236 Chirality : 0.041 0.131 392 Planarity : 0.004 0.033 464 Dihedral : 12.821 137.139 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.37 % Allowed : 10.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.93 (0.47), residues: 327 helix: 2.72 (0.39), residues: 174 sheet: 0.40 (0.69), residues: 50 loop : 1.56 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.015 0.001 PHE A 69 TYR 0.014 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 175) hydrogen bonds : angle 3.79800 ( 489) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.58791 ( 2) covalent geometry : bond 0.00318 ( 2814) covalent geometry : angle 0.45134 ( 3787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.306 Fit side-chains REVERT: B 39 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8165 (mtp85) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2018 time to fit residues: 5.6631 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.184092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126549 restraints weight = 2885.251| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.49 r_work: 0.3208 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2815 Z= 0.096 Angle : 0.410 5.146 3789 Z= 0.214 Chirality : 0.038 0.129 392 Planarity : 0.004 0.035 464 Dihedral : 12.333 134.791 476 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.10 (0.47), residues: 327 helix: 2.87 (0.39), residues: 175 sheet: 0.49 (0.69), residues: 50 loop : 1.58 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 PHE 0.010 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 175) hydrogen bonds : angle 3.61329 ( 489) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.46865 ( 2) covalent geometry : bond 0.00216 ( 2814) covalent geometry : angle 0.40976 ( 3787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.291 Fit side-chains REVERT: B 39 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8119 (mtp85) REVERT: A 44 MET cc_start: 0.7860 (mtt) cc_final: 0.7612 (mtt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2097 time to fit residues: 5.8467 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.184123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126904 restraints weight = 2844.540| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.48 r_work: 0.3263 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2815 Z= 0.101 Angle : 0.419 5.182 3789 Z= 0.220 Chirality : 0.039 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 12.075 133.108 476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.47), residues: 327 helix: 2.86 (0.39), residues: 175 sheet: 0.54 (0.69), residues: 50 loop : 1.55 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 175) hydrogen bonds : angle 3.60853 ( 489) SS BOND : bond 0.00239 ( 1) SS BOND : angle 0.45748 ( 2) covalent geometry : bond 0.00231 ( 2814) covalent geometry : angle 0.41946 ( 3787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.60 seconds wall clock time: 41 minutes 51.30 seconds (2511.30 seconds total)