null Sun 23 Dec 22:23:14 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2inb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:22 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 92 and 0 Target number of residues in the AU: 92 Target solvent content: 0.6597 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 152 Cell parameters: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 29.762 4.000 Wilson plot Bfac: 84.28 1372 reflections ( 99.71 % complete ) and 0 restraints for refining 1244 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3577 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3247 (Rfree = 0.000) for 1244 atoms. Found 5 (5 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 1259 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.224 Round 2: 57 peptides, 9 chains. Longest chain 11 peptides. Score 0.428 Round 3: 58 peptides, 11 chains. Longest chain 11 peptides. Score 0.342 Round 4: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.500 Round 5: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.365 Taking the results from Round 4 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2408 restraints for refining 990 atoms. 2197 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2926 (Rfree = 0.000) for 990 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 2: After refmac, R = 0.3117 (Rfree = 0.000) for 975 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 3: After refmac, R = 0.2865 (Rfree = 0.000) for 967 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2656 (Rfree = 0.000) for 965 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2262 (Rfree = 0.000) for 960 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 994 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.305 Round 2: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.354 Round 3: 70 peptides, 12 chains. Longest chain 10 peptides. Score 0.427 Round 4: 71 peptides, 13 chains. Longest chain 9 peptides. Score 0.393 Round 5: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.482 Taking the results from Round 5 Chains 11, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2399 restraints for refining 986 atoms. 2170 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2737 (Rfree = 0.000) for 986 atoms. Found 1 (4 requested) and removed 11 (2 requested) atoms. Cycle 7: After refmac, R = 0.2541 (Rfree = 0.000) for 975 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 8: After refmac, R = 0.2118 (Rfree = 0.000) for 963 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Cycle 9: After refmac, R = 0.2017 (Rfree = 0.000) for 956 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 955 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 985 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.342 Round 2: 69 peptides, 12 chains. Longest chain 13 peptides. Score 0.417 Round 3: 70 peptides, 11 chains. Longest chain 14 peptides. Score 0.472 Round 4: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.470 Round 5: 69 peptides, 11 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 3 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2363 restraints for refining 1010 atoms. 2104 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2843 (Rfree = 0.000) for 1010 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 12: After refmac, R = 0.2871 (Rfree = 0.000) for 996 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 13: After refmac, R = 0.2991 (Rfree = 0.000) for 989 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 14: After refmac, R = 0.2802 (Rfree = 0.000) for 985 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2708 (Rfree = 0.000) for 983 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 997 seeds are put forward Round 1: 48 peptides, 8 chains. Longest chain 12 peptides. Score 0.376 Round 2: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.459 Round 3: 52 peptides, 8 chains. Longest chain 12 peptides. Score 0.421 Round 4: 51 peptides, 8 chains. Longest chain 9 peptides. Score 0.410 Round 5: 51 peptides, 9 chains. Longest chain 7 peptides. Score 0.360 Taking the results from Round 2 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2436 restraints for refining 1011 atoms. 2241 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 1011 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 17: After refmac, R = 0.2411 (Rfree = 0.000) for 1002 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.2912 (Rfree = 0.000) for 1002 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 19: After refmac, R = 0.2837 (Rfree = 0.000) for 1000 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2659 (Rfree = 0.000) for 1000 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.91 Search for helices and strands: 0 residues in 0 chains, 1029 seeds are put forward Round 1: 39 peptides, 8 chains. Longest chain 6 peptides. Score 0.265 Round 2: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.310 Round 3: 56 peptides, 9 chains. Longest chain 12 peptides. Score 0.417 Round 4: 55 peptides, 10 chains. Longest chain 12 peptides. Score 0.357 Round 5: 59 peptides, 9 chains. Longest chain 12 peptides. Score 0.449 Taking the results from Round 5 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2392 restraints for refining 1011 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2242 (Rfree = 0.000) for 1011 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2429 (Rfree = 0.000) for 1004 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.2301 (Rfree = 0.000) for 1001 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2063 (Rfree = 0.000) for 996 atoms. Found 2 (4 requested) and removed 7 (2 requested) atoms. Cycle 25: After refmac, R = 0.2143 (Rfree = 0.000) for 990 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 1008 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 6 peptides. Score 0.208 Round 2: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.319 Round 3: 59 peptides, 10 chains. Longest chain 13 peptides. Score 0.402 Round 4: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.349 Round 5: 54 peptides, 9 chains. Longest chain 9 peptides. Score 0.395 Taking the results from Round 3 Chains 10, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2458 restraints for refining 998 atoms. 2272 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2765 (Rfree = 0.000) for 998 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2202 (Rfree = 0.000) for 990 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.2092 (Rfree = 0.000) for 989 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.1904 (Rfree = 0.000) for 987 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.1847 (Rfree = 0.000) for 982 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 1013 seeds are put forward Round 1: 41 peptides, 8 chains. Longest chain 6 peptides. Score 0.291 Round 2: 52 peptides, 9 chains. Longest chain 12 peptides. Score 0.372 Round 3: 55 peptides, 7 chains. Longest chain 13 peptides. Score 0.500 Round 4: 53 peptides, 9 chains. Longest chain 7 peptides. Score 0.383 Round 5: 56 peptides, 9 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 3 Chains 7, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2338 restraints for refining 976 atoms. 2153 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2346 (Rfree = 0.000) for 976 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2258 (Rfree = 0.000) for 970 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2091 (Rfree = 0.000) for 968 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.1915 (Rfree = 0.000) for 966 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.1973 (Rfree = 0.000) for 966 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 988 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 7 peptides. Score 0.223 Round 2: 45 peptides, 7 chains. Longest chain 12 peptides. Score 0.393 Round 3: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.365 Round 4: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.329 Round 5: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.353 Taking the results from Round 2 Chains 7, Residues 38, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2401 restraints for refining 979 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2807 (Rfree = 0.000) for 979 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.2362 (Rfree = 0.000) for 972 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.2357 (Rfree = 0.000) for 967 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.2481 (Rfree = 0.000) for 964 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.3174 (Rfree = 0.000) for 963 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.89 Search for helices and strands: 0 residues in 0 chains, 972 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 9 peptides. Score 0.278 Round 2: 42 peptides, 8 chains. Longest chain 12 peptides. Score 0.304 Round 3: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.262 Round 4: 43 peptides, 8 chains. Longest chain 11 peptides. Score 0.316 Round 5: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.275 Taking the results from Round 4 Chains 8, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1372 reflections ( 99.71 % complete ) and 2522 restraints for refining 1008 atoms. 2390 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2705 (Rfree = 0.000) for 1008 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.2014 (Rfree = 0.000) for 1001 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.2005 (Rfree = 0.000) for 997 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Cycle 44: After refmac, R = 0.2654 (Rfree = 0.000) for 989 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2477 (Rfree = 0.000) for 985 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.93 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.238 Round 2: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.265 Round 3: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.333 Round 4: 39 peptides, 7 chains. Longest chain 12 peptides. Score 0.321 Round 5: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.333 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2inb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1372 reflections ( 99.71 % complete ) and 2496 restraints for refining 1006 atoms. 2371 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3065 (Rfree = 0.000) for 1006 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Cycle 47: After refmac, R = 0.2070 (Rfree = 0.000) for 1002 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 48: After refmac, R = 0.2353 (Rfree = 0.000) for 1000 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.1869 (Rfree = 0.000) for 998 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:10 GMT 2018 Job finished. TimeTaking 23.93 Used memory is bytes: 14398216