null Mon 24 Dec 07:34:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2glz-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2glz-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2glz-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:34:12 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/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-noncs/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 297 and 0 Target number of residues in the AU: 297 Target solvent content: 0.5945 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-3.2-parrot-noncs.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-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2448 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 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 3.200 Wilson plot Bfac: 50.12 6969 reflections ( 99.80 % complete ) and 0 restraints for refining 2709 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Starting model: R = 0.3386 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2851 (Rfree = 0.000) for 2709 atoms. Found 21 (24 requested) and removed 169 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.99 2.69 Search for helices and strands: 0 residues in 0 chains, 2590 seeds are put forward NCS extension: 0 residues added, 2590 seeds are put forward Round 1: 151 peptides, 31 chains. Longest chain 8 peptides. Score 0.293 Round 2: 187 peptides, 32 chains. Longest chain 12 peptides. Score 0.425 Round 3: 202 peptides, 30 chains. Longest chain 16 peptides. Score 0.513 Round 4: 195 peptides, 25 chains. Longest chain 21 peptides. Score 0.564 Round 5: 200 peptides, 25 chains. Longest chain 21 peptides. Score 0.580 Taking the results from Round 5 Chains 25, Residues 175, Estimated correctness of the model 35.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4774 restraints for refining 2235 atoms. 4099 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2804 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 2: After refmac, R = 0.2601 (Rfree = 0.000) for 2207 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. Cycle 3: After refmac, R = 0.2555 (Rfree = 0.000) for 2196 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2517 (Rfree = 0.000) for 2191 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2495 (Rfree = 0.000) for 2188 atoms. Found 1 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2293 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2321 seeds are put forward Round 1: 190 peptides, 27 chains. Longest chain 25 peptides. Score 0.517 Round 2: 216 peptides, 24 chains. Longest chain 21 peptides. Score 0.641 Round 3: 216 peptides, 21 chains. Longest chain 28 peptides. Score 0.678 Round 4: 211 peptides, 23 chains. Longest chain 23 peptides. Score 0.640 Round 5: 199 peptides, 22 chains. Longest chain 24 peptides. Score 0.618 Taking the results from Round 3 Chains 23, Residues 195, Estimated correctness of the model 60.4 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4297 restraints for refining 2235 atoms. 3406 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2810 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 7: After refmac, R = 0.2620 (Rfree = 0.000) for 2231 atoms. Found 13 (20 requested) and removed 13 (10 requested) atoms. Cycle 8: After refmac, R = 0.2535 (Rfree = 0.000) for 2222 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 9: After refmac, R = 0.2485 (Rfree = 0.000) for 2219 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2526 (Rfree = 0.000) for 2212 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 2330 seeds are put forward Round 1: 202 peptides, 30 chains. Longest chain 20 peptides. Score 0.513 Round 2: 219 peptides, 26 chains. Longest chain 20 peptides. Score 0.623 Round 3: 216 peptides, 26 chains. Longest chain 29 peptides. Score 0.614 Round 4: 211 peptides, 24 chains. Longest chain 31 peptides. Score 0.626 Round 5: 218 peptides, 25 chains. Longest chain 36 peptides. Score 0.633 Taking the results from Round 5 Chains 27, Residues 193, Estimated correctness of the model 49.7 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4483 restraints for refining 2235 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2829 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 12: After refmac, R = 0.2597 (Rfree = 0.000) for 2232 atoms. Found 8 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2502 (Rfree = 0.000) for 2221 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2467 (Rfree = 0.000) for 2220 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2427 (Rfree = 0.000) for 2213 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 2323 seeds are put forward Round 1: 189 peptides, 28 chains. Longest chain 24 peptides. Score 0.498 Round 2: 211 peptides, 26 chains. Longest chain 26 peptides. Score 0.600 Round 3: 208 peptides, 26 chains. Longest chain 22 peptides. Score 0.590 Round 4: 209 peptides, 27 chains. Longest chain 18 peptides. Score 0.580 Round 5: 199 peptides, 22 chains. Longest chain 27 peptides. Score 0.618 Taking the results from Round 5 Chains 22, Residues 177, Estimated correctness of the model 45.8 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4687 restraints for refining 2235 atoms. 3949 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2723 (Rfree = 0.000) for 2235 atoms. Found 18 (20 requested) and removed 16 (10 requested) atoms. Cycle 17: After refmac, R = 0.2560 (Rfree = 0.000) for 2234 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 18: After refmac, R = 0.2503 (Rfree = 0.000) for 2231 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2453 (Rfree = 0.000) for 2229 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2402 (Rfree = 0.000) for 2226 atoms. Found 10 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.77 Search for helices and strands: 0 residues in 0 chains, 2293 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 2314 seeds are put forward Round 1: 179 peptides, 26 chains. Longest chain 23 peptides. Score 0.494 Round 2: 223 peptides, 24 chains. Longest chain 41 peptides. Score 0.660 Round 3: 214 peptides, 26 chains. Longest chain 27 peptides. Score 0.609 Round 4: 210 peptides, 25 chains. Longest chain 21 peptides. Score 0.610 Round 5: 210 peptides, 22 chains. Longest chain 28 peptides. Score 0.650 Taking the results from Round 2 Chains 26, Residues 199, Estimated correctness of the model 56.2 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4116 restraints for refining 2235 atoms. 3145 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2734 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 22: After refmac, R = 0.2533 (Rfree = 0.000) for 2221 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.2433 (Rfree = 0.000) for 2217 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2376 (Rfree = 0.000) for 2211 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 2207 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 2.70 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2304 seeds are put forward Round 1: 203 peptides, 31 chains. Longest chain 22 peptides. Score 0.501 Round 2: 213 peptides, 27 chains. Longest chain 26 peptides. Score 0.592 Round 3: 206 peptides, 26 chains. Longest chain 25 peptides. Score 0.584 Round 4: 191 peptides, 22 chains. Longest chain 30 peptides. Score 0.594 Round 5: 207 peptides, 25 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 5 Chains 26, Residues 182, Estimated correctness of the model 41.3 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4373 restraints for refining 2235 atoms. 3559 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2662 (Rfree = 0.000) for 2235 atoms. Found 19 (20 requested) and removed 15 (10 requested) atoms. Cycle 27: After refmac, R = 0.2462 (Rfree = 0.000) for 2233 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.2392 (Rfree = 0.000) for 2226 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2331 (Rfree = 0.000) for 2219 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2306 (Rfree = 0.000) for 2209 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 2.67 Search for helices and strands: 0 residues in 0 chains, 2273 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 2286 seeds are put forward Round 1: 195 peptides, 30 chains. Longest chain 20 peptides. Score 0.488 Round 2: 212 peptides, 25 chains. Longest chain 27 peptides. Score 0.616 Round 3: 210 peptides, 28 chains. Longest chain 23 peptides. Score 0.569 Round 4: 206 peptides, 27 chains. Longest chain 32 peptides. Score 0.570 Round 5: 203 peptides, 25 chains. Longest chain 34 peptides. Score 0.589 Taking the results from Round 2 Chains 25, Residues 187, Estimated correctness of the model 45.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4577 restraints for refining 2233 atoms. 3854 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2451 (Rfree = 0.000) for 2233 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.2262 (Rfree = 0.000) for 2234 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.2182 (Rfree = 0.000) for 2230 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2142 (Rfree = 0.000) for 2224 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2081 (Rfree = 0.000) for 2220 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 2.68 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2309 seeds are put forward Round 1: 173 peptides, 30 chains. Longest chain 16 peptides. Score 0.404 Round 2: 187 peptides, 27 chains. Longest chain 25 peptides. Score 0.506 Round 3: 192 peptides, 25 chains. Longest chain 35 peptides. Score 0.554 Round 4: 197 peptides, 26 chains. Longest chain 23 peptides. Score 0.556 Round 5: 199 peptides, 26 chains. Longest chain 31 peptides. Score 0.562 Taking the results from Round 5 Chains 28, Residues 173, Estimated correctness of the model 30.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4450 restraints for refining 2235 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2450 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.2309 (Rfree = 0.000) for 2237 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2190 (Rfree = 0.000) for 2241 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2143 (Rfree = 0.000) for 2237 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 2233 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 2.66 Search for helices and strands: 0 residues in 0 chains, 2306 seeds are put forward NCS extension: 28 residues added (8 deleted due to clashes), 2334 seeds are put forward Round 1: 175 peptides, 27 chains. Longest chain 32 peptides. Score 0.462 Round 2: 193 peptides, 27 chains. Longest chain 29 peptides. Score 0.527 Round 3: 200 peptides, 23 chains. Longest chain 40 peptides. Score 0.608 Round 4: 192 peptides, 21 chains. Longest chain 35 peptides. Score 0.611 Round 5: 188 peptides, 29 chains. Longest chain 20 peptides. Score 0.478 Taking the results from Round 4 Chains 23, Residues 171, Estimated correctness of the model 44.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4297 restraints for refining 2233 atoms. 3530 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2385 (Rfree = 0.000) for 2233 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.2232 (Rfree = 0.000) for 2237 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.2155 (Rfree = 0.000) for 2235 atoms. Found 14 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2088 (Rfree = 0.000) for 2238 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2027 (Rfree = 0.000) for 2232 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 2.68 Search for helices and strands: 0 residues in 0 chains, 2301 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2325 seeds are put forward Round 1: 185 peptides, 26 chains. Longest chain 17 peptides. Score 0.515 Round 2: 199 peptides, 24 chains. Longest chain 32 peptides. Score 0.591 Round 3: 202 peptides, 29 chains. Longest chain 24 peptides. Score 0.528 Round 4: 184 peptides, 25 chains. Longest chain 19 peptides. Score 0.527 Round 5: 179 peptides, 24 chains. Longest chain 31 peptides. Score 0.525 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 175, Estimated correctness of the model 38.6 % 2 chains (28 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2glz-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (175 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6969 reflections ( 99.80 % complete ) and 4332 restraints for refining 2235 atoms. 3535 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2343 (Rfree = 0.000) for 2235 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2291 (Rfree = 0.000) for 2224 atoms. Found 0 (19 requested) and removed 1 (9 requested) atoms. Cycle 48: After refmac, R = 0.2254 (Rfree = 0.000) for 2221 atoms. Found 0 (19 requested) and removed 1 (9 requested) atoms. Cycle 49: After refmac, R = 0.2228 (Rfree = 0.000) for 2220 atoms. Found 0 (19 requested) and removed 2 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:04:37 GMT 2018 Job finished. TimeTaking 30.48 Used memory is bytes: 21268296