Sun 23 Dec 22:22:59 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 2ghr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.8-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/2ghr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.8-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 22:23:08 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/2ghr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-3.8-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 229 and 0 Target number of residues in the AU: 229 Target solvent content: 0.6417 Checking the provided sequence file Detected sequence length: 302 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 302 Adjusted target solvent content: 0.53 Input MTZ file: 2ghr-3.8-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: 91 Cell parameters: 95.828 95.828 75.339 90.000 90.000 90.000 Input sequence file: 2ghr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.65 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: 95.828 3.800 Wilson plot Bfac: 72.86 3738 reflections ( 99.52 % complete ) and 0 restraints for refining 2662 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3324 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3473 (Rfree = 0.000) for 2662 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 2685 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.270 Round 2: 128 peptides, 23 chains. Longest chain 10 peptides. Score 0.360 Round 3: 143 peptides, 20 chains. Longest chain 18 peptides. Score 0.488 Round 4: 160 peptides, 23 chains. Longest chain 18 peptides. Score 0.503 Round 5: 167 peptides, 18 chains. Longest chain 28 peptides. Score 0.615 Taking the results from Round 5 Chains 18, Residues 149, Estimated correctness of the model 5.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4122 restraints for refining 1912 atoms. 3544 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3488 (Rfree = 0.000) for 1912 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 2: After refmac, R = 0.3056 (Rfree = 0.000) for 1878 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 3: After refmac, R = 0.3296 (Rfree = 0.000) for 1851 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.3422 (Rfree = 0.000) for 1816 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.3271 (Rfree = 0.000) for 1800 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 1871 seeds are put forward Round 1: 151 peptides, 26 chains. Longest chain 10 peptides. Score 0.408 Round 2: 161 peptides, 20 chains. Longest chain 23 peptides. Score 0.560 Round 3: 161 peptides, 21 chains. Longest chain 28 peptides. Score 0.543 Round 4: 154 peptides, 18 chains. Longest chain 20 peptides. Score 0.568 Round 5: 161 peptides, 20 chains. Longest chain 21 peptides. Score 0.560 Taking the results from Round 4 Chains 18, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4138 restraints for refining 1877 atoms. 3612 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3009 (Rfree = 0.000) for 1877 atoms. Found 10 (10 requested) and removed 27 (5 requested) atoms. Cycle 7: After refmac, R = 0.2733 (Rfree = 0.000) for 1835 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2683 (Rfree = 0.000) for 1809 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2570 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2669 (Rfree = 0.000) for 1792 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 1876 seeds are put forward Round 1: 152 peptides, 24 chains. Longest chain 13 peptides. Score 0.451 Round 2: 161 peptides, 21 chains. Longest chain 19 peptides. Score 0.543 Round 3: 154 peptides, 20 chains. Longest chain 20 peptides. Score 0.533 Round 4: 166 peptides, 22 chains. Longest chain 15 peptides. Score 0.545 Round 5: 170 peptides, 21 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 5 Chains 21, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4271 restraints for refining 1965 atoms. 3696 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2956 (Rfree = 0.000) for 1965 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2690 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.2611 (Rfree = 0.000) for 1939 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2620 (Rfree = 0.000) for 1929 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2515 (Rfree = 0.000) for 1920 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.36 Search for helices and strands: 0 residues in 0 chains, 2016 seeds are put forward Round 1: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.391 Round 2: 169 peptides, 21 chains. Longest chain 23 peptides. Score 0.573 Round 3: 169 peptides, 21 chains. Longest chain 21 peptides. Score 0.573 Round 4: 175 peptides, 23 chains. Longest chain 31 peptides. Score 0.562 Round 5: 175 peptides, 20 chains. Longest chain 32 peptides. Score 0.610 Taking the results from Round 5 Chains 21, Residues 155, Estimated correctness of the model 3.5 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4376 restraints for refining 2106 atoms. 3663 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3042 (Rfree = 0.000) for 2106 atoms. Found 11 (11 requested) and removed 38 (5 requested) atoms. Cycle 17: After refmac, R = 0.2935 (Rfree = 0.000) for 2046 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 18: After refmac, R = 0.2452 (Rfree = 0.000) for 2021 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2448 (Rfree = 0.000) for 2007 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2613 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 2054 seeds are put forward Round 1: 144 peptides, 24 chains. Longest chain 10 peptides. Score 0.415 Round 2: 156 peptides, 25 chains. Longest chain 11 peptides. Score 0.449 Round 3: 157 peptides, 23 chains. Longest chain 12 peptides. Score 0.491 Round 4: 155 peptides, 21 chains. Longest chain 12 peptides. Score 0.519 Round 5: 160 peptides, 19 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 5 Chains 19, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4924 restraints for refining 2160 atoms. 4379 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2880 (Rfree = 0.000) for 2160 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 22: After refmac, R = 0.2700 (Rfree = 0.000) for 2117 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2704 (Rfree = 0.000) for 2099 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2535 (Rfree = 0.000) for 2091 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.2470 (Rfree = 0.000) for 2078 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.327 Round 2: 139 peptides, 22 chains. Longest chain 17 peptides. Score 0.432 Round 3: 128 peptides, 21 chains. Longest chain 15 peptides. Score 0.402 Round 4: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.432 Round 5: 141 peptides, 22 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 5 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 5104 restraints for refining 2185 atoms. 4650 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2838 (Rfree = 0.000) for 2185 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 27: After refmac, R = 0.2833 (Rfree = 0.000) for 2155 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.2749 (Rfree = 0.000) for 2135 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.2699 (Rfree = 0.000) for 2120 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2499 (Rfree = 0.000) for 2117 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 2188 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 7 peptides. Score 0.263 Round 2: 140 peptides, 23 chains. Longest chain 12 peptides. Score 0.417 Round 3: 145 peptides, 25 chains. Longest chain 13 peptides. Score 0.400 Round 4: 143 peptides, 21 chains. Longest chain 14 peptides. Score 0.469 Round 5: 136 peptides, 22 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 4 Chains 22, Residues 122, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4787 restraints for refining 2157 atoms. 4278 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3045 (Rfree = 0.000) for 2157 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 32: After refmac, R = 0.2576 (Rfree = 0.000) for 2133 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 2117 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 34: After refmac, R = 0.2249 (Rfree = 0.000) for 2106 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2130 (Rfree = 0.000) for 2102 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 2170 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.335 Round 2: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.408 Round 3: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.411 Round 4: 138 peptides, 20 chains. Longest chain 19 peptides. Score 0.467 Round 5: 132 peptides, 20 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 4 Chains 21, Residues 118, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 5038 restraints for refining 2183 atoms. 4553 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2601 (Rfree = 0.000) for 2183 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.2368 (Rfree = 0.000) for 2160 atoms. Found 6 (11 requested) and removed 16 (5 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 2137 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2279 (Rfree = 0.000) for 2129 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1910 (Rfree = 0.000) for 2122 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 2172 seeds are put forward Round 1: 114 peptides, 21 chains. Longest chain 13 peptides. Score 0.333 Round 2: 135 peptides, 21 chains. Longest chain 13 peptides. Score 0.434 Round 3: 143 peptides, 22 chains. Longest chain 11 peptides. Score 0.450 Round 4: 137 peptides, 19 chains. Longest chain 15 peptides. Score 0.482 Round 5: 143 peptides, 22 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 4 Chains 19, Residues 118, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3738 reflections ( 99.52 % complete ) and 4803 restraints for refining 2173 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2666 (Rfree = 0.000) for 2173 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 42: After refmac, R = 0.2480 (Rfree = 0.000) for 2149 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2668 (Rfree = 0.000) for 2138 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2334 (Rfree = 0.000) for 2127 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1979 (Rfree = 0.000) for 2118 atoms. Found 0 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 2169 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 10 peptides. Score 0.246 Round 2: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.317 Round 3: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.375 Round 4: 125 peptides, 23 chains. Longest chain 11 peptides. Score 0.345 Round 5: 131 peptides, 21 chains. Longest chain 14 peptides. Score 0.416 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 110, 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 2ghr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3738 reflections ( 99.52 % complete ) and 4904 restraints for refining 2105 atoms. 4485 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2366 (Rfree = 0.000) for 2105 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2510 (Rfree = 0.000) for 2089 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2529 (Rfree = 0.000) for 2070 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2157 (Rfree = 0.000) for 2058 atoms. TimeTaking 44.32