null Sun 23 Dec 22:22:46 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 2hhz-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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/2hhz-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 22:22:56 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/2hhz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 91 and 0 Target number of residues in the AU: 91 Target solvent content: 0.6658 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 150 Adjusted target solvent content: 0.45 Input MTZ file: 2hhz-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: 96 Cell parameters: 71.030 71.030 58.410 90.000 90.000 90.000 Input sequence file: 2hhz-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1200 target number of atoms Had to go as low as 0.75 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: 50.226 4.003 Wilson plot Bfac: 87.63 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1420 reflections ( 99.30 % complete ) and 0 restraints for refining 1336 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3594 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3061 (Rfree = 0.000) for 1336 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 4.03 Search for helices and strands: 0 residues in 0 chains, 1359 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.193 Round 2: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.290 Round 3: 69 peptides, 14 chains. Longest chain 8 peptides. Score 0.323 Round 4: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.447 Round 5: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.436 Taking the results from Round 4 Chains 12, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2570 restraints for refining 1075 atoms. 2342 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3039 (Rfree = 0.000) for 1075 atoms. Found 5 (5 requested) and removed 38 (2 requested) atoms. Cycle 2: After refmac, R = 0.2838 (Rfree = 0.000) for 1017 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 3: After refmac, R = 0.2262 (Rfree = 0.000) for 995 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 986 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.1941 (Rfree = 0.000) for 982 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.76 4.02 Search for helices and strands: 0 residues in 0 chains, 1016 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 6 peptides. Score 0.256 Round 2: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.325 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.419 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.372 Round 5: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.460 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2170 restraints for refining 993 atoms. 1917 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 993 atoms. Found 3 (4 requested) and removed 35 (2 requested) atoms. Cycle 7: After refmac, R = 0.1997 (Rfree = 0.000) for 952 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. Cycle 8: After refmac, R = 0.2080 (Rfree = 0.000) for 937 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. Cycle 9: After refmac, R = 0.1850 (Rfree = 0.000) for 927 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.1867 (Rfree = 0.000) for 922 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 4.05 Search for helices and strands: 0 residues in 0 chains, 971 seeds are put forward Round 1: 63 peptides, 13 chains. Longest chain 6 peptides. Score 0.302 Round 2: 59 peptides, 13 chains. Longest chain 6 peptides. Score 0.254 Round 3: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.410 Round 4: 68 peptides, 11 chains. Longest chain 10 peptides. Score 0.450 Round 5: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.496 Taking the results from Round 5 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2610 restraints for refining 1067 atoms. 2362 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2484 (Rfree = 0.000) for 1067 atoms. Found 4 (5 requested) and removed 18 (2 requested) atoms. Cycle 12: After refmac, R = 0.2244 (Rfree = 0.000) for 1039 atoms. Found 0 (4 requested) and removed 11 (2 requested) atoms. Cycle 13: After refmac, R = 0.1819 (Rfree = 0.000) for 1020 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.1485 (Rfree = 0.000) for 1010 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 15: After refmac, R = 0.1551 (Rfree = 0.000) for 1005 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 4.08 Search for helices and strands: 0 residues in 0 chains, 1041 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.243 Round 2: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Round 3: 60 peptides, 11 chains. Longest chain 10 peptides. Score 0.364 Round 4: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.426 Round 5: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.421 Taking the results from Round 4 Chains 12, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2331 restraints for refining 1026 atoms. 2111 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 1026 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Cycle 17: After refmac, R = 0.2259 (Rfree = 0.000) for 997 atoms. Found 2 (4 requested) and removed 10 (2 requested) atoms. Cycle 18: After refmac, R = 0.2296 (Rfree = 0.000) for 989 atoms. Found 0 (4 requested) and removed 9 (2 requested) atoms. Cycle 19: After refmac, R = 0.2248 (Rfree = 0.000) for 980 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2417 (Rfree = 0.000) for 975 atoms. Found 0 (4 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 4.02 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 62 peptides, 12 chains. Longest chain 11 peptides. Score 0.339 Round 2: 61 peptides, 11 chains. Longest chain 12 peptides. Score 0.375 Round 3: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.468 Round 4: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.386 Round 5: 61 peptides, 11 chains. Longest chain 8 peptides. Score 0.375 Taking the results from Round 3 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2500 restraints for refining 1047 atoms. 2301 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2314 (Rfree = 0.000) for 1047 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 22: After refmac, R = 0.1960 (Rfree = 0.000) for 1036 atoms. Found 0 (4 requested) and removed 10 (2 requested) atoms. Cycle 23: After refmac, R = 0.1825 (Rfree = 0.000) for 1024 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.1898 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 25: After refmac, R = 0.1671 (Rfree = 0.000) for 1025 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 4.08 Search for helices and strands: 0 residues in 0 chains, 1063 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.253 Round 2: 55 peptides, 12 chains. Longest chain 5 peptides. Score 0.256 Round 3: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.257 Round 4: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.243 Round 5: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.353 Taking the results from Round 5 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2638 restraints for refining 1084 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1739 (Rfree = 0.000) for 1084 atoms. Found 1 (5 requested) and removed 9 (2 requested) atoms. Cycle 27: After refmac, R = 0.1984 (Rfree = 0.000) for 1071 atoms. Found 3 (5 requested) and removed 11 (2 requested) atoms. Cycle 28: After refmac, R = 0.2073 (Rfree = 0.000) for 1060 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 29: After refmac, R = 0.2356 (Rfree = 0.000) for 1052 atoms. Found 4 (4 requested) and removed 25 (2 requested) atoms. Cycle 30: After refmac, R = 0.2282 (Rfree = 0.000) for 1027 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.93 Search for helices and strands: 0 residues in 0 chains, 1063 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.212 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.249 Round 3: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.328 Round 4: 48 peptides, 8 chains. Longest chain 15 peptides. Score 0.375 Round 5: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.340 Taking the results from Round 4 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2452 restraints for refining 1036 atoms. 2300 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2120 (Rfree = 0.000) for 1036 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 32: After refmac, R = 0.2039 (Rfree = 0.000) for 1026 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Cycle 33: After refmac, R = 0.1763 (Rfree = 0.000) for 999 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.1209 (Rfree = 0.000) for 999 atoms. Found 1 (4 requested) and removed 11 (2 requested) atoms. Cycle 35: After refmac, R = 0.1294 (Rfree = 0.000) for 989 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 4.04 Search for helices and strands: 0 residues in 0 chains, 1026 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.194 Round 2: 38 peptides, 8 chains. Longest chain 6 peptides. Score 0.251 Round 3: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.312 Round 4: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.371 Round 5: 53 peptides, 8 chains. Longest chain 9 peptides. Score 0.431 Taking the results from Round 5 Chains 8, Residues 45, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2338 restraints for refining 1053 atoms. 2132 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1708 (Rfree = 0.000) for 1053 atoms. Found 2 (4 requested) and removed 13 (2 requested) atoms. Cycle 37: After refmac, R = 0.2298 (Rfree = 0.000) for 1028 atoms. Found 4 (4 requested) and removed 21 (2 requested) atoms. Cycle 38: After refmac, R = 0.1813 (Rfree = 0.000) for 1009 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 39: After refmac, R = 0.2130 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 18 (2 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 988 atoms. Found 4 (4 requested) and removed 17 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 4.07 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 6 peptides. Score 0.208 Round 2: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.247 Round 3: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.371 Round 4: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.333 Round 5: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.324 Taking the results from Round 3 Chains 9, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1420 reflections ( 99.30 % complete ) and 2116 restraints for refining 969 atoms. 1953 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1753 (Rfree = 0.000) for 969 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.1643 (Rfree = 0.000) for 960 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 43: After refmac, R = 0.1294 (Rfree = 0.000) for 953 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.1424 (Rfree = 0.000) for 950 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.1235 (Rfree = 0.000) for 946 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.98 Search for helices and strands: 0 residues in 0 chains, 969 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.238 Round 2: 48 peptides, 9 chains. Longest chain 10 peptides. Score 0.324 Round 3: 52 peptides, 10 chains. Longest chain 7 peptides. Score 0.321 Round 4: 51 peptides, 9 chains. Longest chain 8 peptides. Score 0.359 Round 5: 54 peptides, 10 chains. Longest chain 7 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 42, 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 2hhz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1420 reflections ( 99.30 % complete ) and 2303 restraints for refining 1023 atoms. 2144 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1572 (Rfree = 0.000) for 1023 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1555 (Rfree = 0.000) for 1020 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1569 (Rfree = 0.000) for 1018 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1360 (Rfree = 0.000) for 1016 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:46:29 GMT 2018 Job finished. TimeTaking 23.71 Used memory is bytes: 3114712