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 2glz-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2glz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.6-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/2glz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.6-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 19:28:13 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/2glz-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2glz-3.6-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 277 and 0 Target number of residues in the AU: 277 Target solvent content: 0.6218 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.58 Input MTZ file: 2glz-3.6-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: 19 Cell parameters: 46.427 84.786 100.702 90.000 90.000 90.000 Input sequence file: 2glz-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.85 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.894 3.600 Wilson plot Bfac: 61.87 4925 reflections ( 99.72 % complete ) and 0 restraints for refining 2716 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3422 (Rfree = 0.000) for 2716 atoms. Found 17 (17 requested) and removed 40 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.99 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward NCS extension: 0 residues added, 2753 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 8 peptides. Score 0.326 Round 2: 173 peptides, 25 chains. Longest chain 22 peptides. Score 0.488 Round 3: 180 peptides, 24 chains. Longest chain 20 peptides. Score 0.529 Round 4: 182 peptides, 25 chains. Longest chain 16 peptides. Score 0.520 Round 5: 191 peptides, 27 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 3 Chains 25, Residues 156, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4754 restraints for refining 2218 atoms. 4100 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3017 (Rfree = 0.000) for 2218 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2845 (Rfree = 0.000) for 2172 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2448 (Rfree = 0.000) for 2142 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.2682 (Rfree = 0.000) for 2119 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 5: After refmac, R = 0.2729 (Rfree = 0.000) for 2102 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 2196 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2222 seeds are put forward Round 1: 162 peptides, 28 chains. Longest chain 14 peptides. Score 0.395 Round 2: 180 peptides, 24 chains. Longest chain 23 peptides. Score 0.529 Round 3: 192 peptides, 24 chains. Longest chain 23 peptides. Score 0.569 Round 4: 180 peptides, 25 chains. Longest chain 20 peptides. Score 0.513 Round 5: 170 peptides, 21 chains. Longest chain 19 peptides. Score 0.541 Taking the results from Round 3 Chains 26, Residues 168, Estimated correctness of the model 2.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4822 restraints for refining 2219 atoms. 4135 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2970 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2745 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 8: After refmac, R = 0.2760 (Rfree = 0.000) for 2167 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.2600 (Rfree = 0.000) for 2155 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 10: After refmac, R = 0.2612 (Rfree = 0.000) for 2146 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.95 Search for helices and strands: 0 residues in 0 chains, 2223 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 2261 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 12 peptides. Score 0.359 Round 2: 176 peptides, 26 chains. Longest chain 21 peptides. Score 0.483 Round 3: 190 peptides, 27 chains. Longest chain 23 peptides. Score 0.517 Round 4: 190 peptides, 26 chains. Longest chain 24 peptides. Score 0.532 Round 5: 190 peptides, 29 chains. Longest chain 23 peptides. Score 0.486 Taking the results from Round 4 Chains 29, Residues 164, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4653 restraints for refining 2218 atoms. 3941 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2869 (Rfree = 0.000) for 2218 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 12: After refmac, R = 0.2763 (Rfree = 0.000) for 2187 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.2695 (Rfree = 0.000) for 2177 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 14: After refmac, R = 0.2583 (Rfree = 0.000) for 2159 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2598 (Rfree = 0.000) for 2148 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 2.89 Search for helices and strands: 0 residues in 0 chains, 2236 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2258 seeds are put forward Round 1: 161 peptides, 26 chains. Longest chain 22 peptides. Score 0.425 Round 2: 172 peptides, 25 chains. Longest chain 21 peptides. Score 0.484 Round 3: 199 peptides, 29 chains. Longest chain 17 peptides. Score 0.517 Round 4: 192 peptides, 24 chains. Longest chain 25 peptides. Score 0.569 Round 5: 184 peptides, 27 chains. Longest chain 23 peptides. Score 0.496 Taking the results from Round 4 Chains 25, Residues 168, Estimated correctness of the model 2.2 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4609 restraints for refining 2219 atoms. 3903 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2768 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.2801 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 18: After refmac, R = 0.2606 (Rfree = 0.000) for 2181 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2134 (Rfree = 0.000) for 2177 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2076 (Rfree = 0.000) for 2171 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.95 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2276 seeds are put forward Round 1: 147 peptides, 27 chains. Longest chain 10 peptides. Score 0.350 Round 2: 177 peptides, 26 chains. Longest chain 19 peptides. Score 0.486 Round 3: 181 peptides, 26 chains. Longest chain 19 peptides. Score 0.501 Round 4: 185 peptides, 24 chains. Longest chain 22 peptides. Score 0.546 Round 5: 185 peptides, 27 chains. Longest chain 19 peptides. Score 0.499 Taking the results from Round 4 Chains 24, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4911 restraints for refining 2219 atoms. 4291 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2803 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 22: After refmac, R = 0.2764 (Rfree = 0.000) for 2201 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 23: After refmac, R = 0.2815 (Rfree = 0.000) for 2188 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 24: After refmac, R = 0.2534 (Rfree = 0.000) for 2171 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2520 (Rfree = 0.000) for 2164 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.98 Search for helices and strands: 0 residues in 0 chains, 2279 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2304 seeds are put forward Round 1: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.381 Round 2: 178 peptides, 27 chains. Longest chain 15 peptides. Score 0.474 Round 3: 183 peptides, 29 chains. Longest chain 16 peptides. Score 0.460 Round 4: 175 peptides, 25 chains. Longest chain 21 peptides. Score 0.495 Round 5: 178 peptides, 26 chains. Longest chain 20 peptides. Score 0.490 Taking the results from Round 4 Chains 25, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4869 restraints for refining 2219 atoms. 4294 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2672 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 27: After refmac, R = 0.2601 (Rfree = 0.000) for 2209 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2499 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 29: After refmac, R = 0.2692 (Rfree = 0.000) for 2189 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 30: After refmac, R = 0.2607 (Rfree = 0.000) for 2178 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2300 seeds are put forward Round 1: 158 peptides, 31 chains. Longest chain 11 peptides. Score 0.324 Round 2: 156 peptides, 22 chains. Longest chain 20 peptides. Score 0.474 Round 3: 162 peptides, 23 chains. Longest chain 14 peptides. Score 0.480 Round 4: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.456 Round 5: 163 peptides, 23 chains. Longest chain 22 peptides. Score 0.484 Taking the results from Round 5 Chains 23, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 4973 restraints for refining 2219 atoms. 4436 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2882 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2827 (Rfree = 0.000) for 2202 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 33: After refmac, R = 0.2634 (Rfree = 0.000) for 2185 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 34: After refmac, R = 0.2625 (Rfree = 0.000) for 2174 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.2637 (Rfree = 0.000) for 2170 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2254 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2287 seeds are put forward Round 1: 122 peptides, 24 chains. Longest chain 11 peptides. Score 0.296 Round 2: 141 peptides, 24 chains. Longest chain 13 peptides. Score 0.379 Round 3: 147 peptides, 24 chains. Longest chain 14 peptides. Score 0.404 Round 4: 144 peptides, 25 chains. Longest chain 11 peptides. Score 0.374 Round 5: 154 peptides, 23 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 5 Chains 23, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4925 reflections ( 99.72 % complete ) and 4982 restraints for refining 2219 atoms. 4481 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2811 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 37: After refmac, R = 0.2699 (Rfree = 0.000) for 2197 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 38: After refmac, R = 0.2771 (Rfree = 0.000) for 2186 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2886 (Rfree = 0.000) for 2176 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2646 (Rfree = 0.000) for 2165 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.95 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 2292 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 10 peptides. Score 0.286 Round 2: 143 peptides, 24 chains. Longest chain 11 peptides. Score 0.388 Round 3: 141 peptides, 21 chains. Longest chain 12 peptides. Score 0.434 Round 4: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.378 Round 5: 144 peptides, 23 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 3 Chains 21, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4925 reflections ( 99.72 % complete ) and 5041 restraints for refining 2219 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2870 (Rfree = 0.000) for 2219 atoms. Found 14 (14 requested) and removed 20 (7 requested) atoms. Cycle 42: After refmac, R = 0.2871 (Rfree = 0.000) for 2205 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.2856 (Rfree = 0.000) for 2198 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.2750 (Rfree = 0.000) for 2192 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.2602 (Rfree = 0.000) for 2185 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 2.96 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2303 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.249 Round 2: 143 peptides, 27 chains. Longest chain 8 peptides. Score 0.332 Round 3: 145 peptides, 24 chains. Longest chain 11 peptides. Score 0.396 Round 4: 135 peptides, 23 chains. Longest chain 13 peptides. Score 0.372 Round 5: 131 peptides, 23 chains. Longest chain 9 peptides. Score 0.355 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 121, 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 2glz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4925 reflections ( 99.72 % complete ) and 4932 restraints for refining 2218 atoms. 4472 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2831 (Rfree = 0.000) for 2218 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2752 (Rfree = 0.000) for 2196 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2825 (Rfree = 0.000) for 2175 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2757 (Rfree = 0.000) for 2161 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:24:17 GMT 2018 Job finished. TimeTaking 56.34