null Tue 25 Dec 19:27:57 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 2gno-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.4-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/2gno-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.4-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 ============================================================ Tue 25 Dec 19:28:06 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/2gno-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-3.4-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 204 and 0 Target number of residues in the AU: 204 Target solvent content: 0.6621 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-3.4-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 target number of atoms Had to go as low as 0.70 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: 95.855 3.400 Wilson plot Bfac: 86.12 4642 reflections ( 99.10 % complete ) and 0 restraints for refining 2714 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3389 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2309 (Rfree = 0.000) for 2714 atoms. Found 6 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 2768 seeds are put forward Round 1: 141 peptides, 24 chains. Longest chain 11 peptides. Score 0.412 Round 2: 176 peptides, 24 chains. Longest chain 19 peptides. Score 0.564 Round 3: 176 peptides, 23 chains. Longest chain 19 peptides. Score 0.581 Round 4: 189 peptides, 25 chains. Longest chain 28 peptides. Score 0.596 Round 5: 177 peptides, 22 chains. Longest chain 18 peptides. Score 0.602 Taking the results from Round 5 Chains 22, Residues 155, Estimated correctness of the model 29.3 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 4999 restraints for refining 2219 atoms. 4328 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2962 (Rfree = 0.000) for 2219 atoms. Found 7 (16 requested) and removed 20 (8 requested) atoms. Cycle 2: After refmac, R = 0.2797 (Rfree = 0.000) for 2180 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2659 (Rfree = 0.000) for 2165 atoms. Found 0 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2568 (Rfree = 0.000) for 2140 atoms. Found 5 (16 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2457 (Rfree = 0.000) for 2128 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 142 peptides, 24 chains. Longest chain 13 peptides. Score 0.416 Round 2: 176 peptides, 26 chains. Longest chain 15 peptides. Score 0.529 Round 3: 193 peptides, 25 chains. Longest chain 29 peptides. Score 0.611 Round 4: 188 peptides, 26 chains. Longest chain 19 peptides. Score 0.576 Round 5: 179 peptides, 21 chains. Longest chain 29 peptides. Score 0.625 Taking the results from Round 5 Chains 21, Residues 158, Estimated correctness of the model 36.6 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 4623 restraints for refining 2177 atoms. 3889 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2828 (Rfree = 0.000) for 2177 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. Cycle 7: After refmac, R = 0.2647 (Rfree = 0.000) for 2161 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2512 (Rfree = 0.000) for 2153 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2462 (Rfree = 0.000) for 2138 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2401 (Rfree = 0.000) for 2128 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 162 peptides, 26 chains. Longest chain 20 peptides. Score 0.469 Round 2: 169 peptides, 25 chains. Longest chain 15 peptides. Score 0.518 Round 3: 184 peptides, 24 chains. Longest chain 23 peptides. Score 0.594 Round 4: 177 peptides, 23 chains. Longest chain 22 peptides. Score 0.585 Round 5: 182 peptides, 23 chains. Longest chain 26 peptides. Score 0.603 Taking the results from Round 5 Chains 23, Residues 159, Estimated correctness of the model 29.7 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 4735 restraints for refining 2219 atoms. 4025 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2794 (Rfree = 0.000) for 2219 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2850 (Rfree = 0.000) for 2180 atoms. Found 7 (16 requested) and removed 15 (8 requested) atoms. Cycle 13: After refmac, R = 0.2566 (Rfree = 0.000) for 2155 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2198 (Rfree = 0.000) for 2131 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2509 (Rfree = 0.000) for 2119 atoms. Found 11 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward Round 1: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.420 Round 2: 167 peptides, 23 chains. Longest chain 29 peptides. Score 0.546 Round 3: 171 peptides, 22 chains. Longest chain 23 peptides. Score 0.579 Round 4: 181 peptides, 24 chains. Longest chain 12 peptides. Score 0.583 Round 5: 173 peptides, 22 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 5 Chains 22, Residues 151, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 4953 restraints for refining 2219 atoms. 4371 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2699 (Rfree = 0.000) for 2219 atoms. Found 16 (16 requested) and removed 33 (8 requested) atoms. Cycle 17: After refmac, R = 0.2755 (Rfree = 0.000) for 2188 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 18: After refmac, R = 0.2116 (Rfree = 0.000) for 2177 atoms. Found 13 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2184 (Rfree = 0.000) for 2178 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.1766 (Rfree = 0.000) for 2177 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 2291 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 11 peptides. Score 0.295 Round 2: 163 peptides, 28 chains. Longest chain 13 peptides. Score 0.434 Round 3: 170 peptides, 25 chains. Longest chain 14 peptides. Score 0.522 Round 4: 167 peptides, 24 chains. Longest chain 15 peptides. Score 0.528 Round 5: 174 peptides, 24 chains. Longest chain 25 peptides. Score 0.556 Taking the results from Round 5 Chains 24, Residues 150, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 4973 restraints for refining 2219 atoms. 4397 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 2219 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.2102 (Rfree = 0.000) for 2207 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.1846 (Rfree = 0.000) for 2193 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1578 (Rfree = 0.000) for 2184 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.1757 (Rfree = 0.000) for 2178 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward Round 1: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.376 Round 2: 145 peptides, 23 chains. Longest chain 13 peptides. Score 0.451 Round 3: 161 peptides, 23 chains. Longest chain 20 peptides. Score 0.521 Round 4: 165 peptides, 24 chains. Longest chain 15 peptides. Score 0.520 Round 5: 159 peptides, 23 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 3 Chains 23, Residues 138, Estimated correctness of the model 0.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 5049 restraints for refining 2219 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2132 (Rfree = 0.000) for 2219 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.2407 (Rfree = 0.000) for 2210 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.1638 (Rfree = 0.000) for 2202 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1593 (Rfree = 0.000) for 2197 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1561 (Rfree = 0.000) for 2188 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward Round 1: 147 peptides, 26 chains. Longest chain 14 peptides. Score 0.399 Round 2: 155 peptides, 25 chains. Longest chain 14 peptides. Score 0.457 Round 3: 145 peptides, 20 chains. Longest chain 14 peptides. Score 0.510 Round 4: 152 peptides, 20 chains. Longest chain 14 peptides. Score 0.540 Round 5: 159 peptides, 23 chains. Longest chain 14 peptides. Score 0.513 Taking the results from Round 4 Chains 20, Residues 132, Estimated correctness of the model 7.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 5012 restraints for refining 2219 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1919 (Rfree = 0.000) for 2219 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.1846 (Rfree = 0.000) for 2212 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2216 (Rfree = 0.000) for 2206 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 34: After refmac, R = 0.1669 (Rfree = 0.000) for 2210 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.1568 (Rfree = 0.000) for 2208 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 10 peptides. Score 0.296 Round 2: 137 peptides, 24 chains. Longest chain 11 peptides. Score 0.392 Round 3: 146 peptides, 25 chains. Longest chain 12 peptides. Score 0.415 Round 4: 134 peptides, 21 chains. Longest chain 13 peptides. Score 0.441 Round 5: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 5257 restraints for refining 2216 atoms. 4811 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2023 (Rfree = 0.000) for 2216 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.1755 (Rfree = 0.000) for 2211 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.1718 (Rfree = 0.000) for 2203 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2141 (Rfree = 0.000) for 2198 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.2499 (Rfree = 0.000) for 2201 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward Round 1: 117 peptides, 21 chains. Longest chain 9 peptides. Score 0.356 Round 2: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.395 Round 3: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.421 Round 4: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.389 Round 5: 118 peptides, 19 chains. Longest chain 11 peptides. Score 0.406 Taking the results from Round 3 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4642 reflections ( 99.10 % complete ) and 5093 restraints for refining 2219 atoms. 4678 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2068 (Rfree = 0.000) for 2219 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1771 (Rfree = 0.000) for 2215 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.1867 (Rfree = 0.000) for 2211 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1829 (Rfree = 0.000) for 2207 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1843 (Rfree = 0.000) for 2205 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 10 peptides. Score 0.273 Round 2: 120 peptides, 20 chains. Longest chain 10 peptides. Score 0.394 Round 3: 128 peptides, 20 chains. Longest chain 12 peptides. Score 0.433 Round 4: 135 peptides, 20 chains. Longest chain 14 peptides. Score 0.466 Round 5: 131 peptides, 19 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 112, 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 2gno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4642 reflections ( 99.10 % complete ) and 5129 restraints for refining 2219 atoms. 4700 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1917 (Rfree = 0.000) for 2219 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2013 (Rfree = 0.000) for 2207 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1904 (Rfree = 0.000) for 2196 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1797 (Rfree = 0.000) for 2182 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:19 GMT 2018 Job finished. TimeTaking 48.37 Used memory is bytes: 11714560