Mon 24 Dec 01:05:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2glz-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2glz-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-mrncs ############### 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 01:05:23 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/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2glz-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 2701 atoms. Observations/parameters ratio is 0.65 ------------------------------------------------------ Starting model: R = 0.3299 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2588 (Rfree = 0.000) for 2701 atoms. Found 13 (24 requested) and removed 142 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 2.73 Search for helices and strands: 0 residues in 0 chains, 2606 seeds are put forward NCS extension: 0 residues added, 2606 seeds are put forward Round 1: 174 peptides, 34 chains. Longest chain 11 peptides. Score 0.338 Round 2: 194 peptides, 29 chains. Longest chain 16 peptides. Score 0.500 Round 3: 193 peptides, 30 chains. Longest chain 16 peptides. Score 0.480 Round 4: 204 peptides, 28 chains. Longest chain 21 peptides. Score 0.549 Round 5: 209 peptides, 27 chains. Longest chain 32 peptides. Score 0.580 Taking the results from Round 5 Chains 29, Residues 182, Estimated correctness of the model 35.6 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4537 restraints for refining 2235 atoms. 3772 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2953 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 2: After refmac, R = 0.2741 (Rfree = 0.000) for 2200 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 3: After refmac, R = 0.2615 (Rfree = 0.000) for 2183 atoms. Found 15 (19 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2512 (Rfree = 0.000) for 2180 atoms. Found 3 (19 requested) and removed 14 (9 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 2167 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 2.73 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2278 seeds are put forward Round 1: 199 peptides, 30 chains. Longest chain 18 peptides. Score 0.502 Round 2: 208 peptides, 26 chains. Longest chain 32 peptides. Score 0.590 Round 3: 224 peptides, 25 chains. Longest chain 22 peptides. Score 0.650 Round 4: 219 peptides, 24 chains. Longest chain 21 peptides. Score 0.649 Round 5: 223 peptides, 25 chains. Longest chain 28 peptides. Score 0.647 Taking the results from Round 3 Chains 26, Residues 199, Estimated correctness of the model 53.8 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4387 restraints for refining 2235 atoms. 3498 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2812 (Rfree = 0.000) for 2235 atoms. Found 13 (20 requested) and removed 15 (10 requested) atoms. Cycle 7: After refmac, R = 0.2647 (Rfree = 0.000) for 2220 atoms. Found 15 (20 requested) and removed 18 (10 requested) atoms. Cycle 8: After refmac, R = 0.2478 (Rfree = 0.000) for 2214 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2408 (Rfree = 0.000) for 2205 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 10: After refmac, R = 0.2363 (Rfree = 0.000) for 2197 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 2.69 Search for helices and strands: 0 residues in 0 chains, 2276 seeds are put forward NCS extension: 24 residues added (7 deleted due to clashes), 2300 seeds are put forward Round 1: 223 peptides, 29 chains. Longest chain 23 peptides. Score 0.595 Round 2: 219 peptides, 20 chains. Longest chain 34 peptides. Score 0.697 Round 3: 222 peptides, 21 chains. Longest chain 67 peptides. Score 0.693 Round 4: 224 peptides, 23 chains. Longest chain 42 peptides. Score 0.674 Round 5: 223 peptides, 24 chains. Longest chain 29 peptides. Score 0.660 Taking the results from Round 2 Chains 20, Residues 199, Estimated correctness of the model 64.5 % 3 chains (74 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3880 restraints for refining 2235 atoms. 2811 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2767 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 12: After refmac, R = 0.2538 (Rfree = 0.000) for 2224 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.2448 (Rfree = 0.000) for 2209 atoms. Found 1 (19 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2399 (Rfree = 0.000) for 2197 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2347 (Rfree = 0.000) for 2187 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.68 Search for helices and strands: 0 residues in 0 chains, 2262 seeds are put forward NCS extension: 40 residues added (6 deleted due to clashes), 2302 seeds are put forward Round 1: 217 peptides, 27 chains. Longest chain 31 peptides. Score 0.604 Round 2: 222 peptides, 22 chains. Longest chain 51 peptides. Score 0.681 Round 3: 226 peptides, 21 chains. Longest chain 43 peptides. Score 0.703 Round 4: 215 peptides, 20 chains. Longest chain 28 peptides. Score 0.687 Round 5: 214 peptides, 20 chains. Longest chain 28 peptides. Score 0.685 Taking the results from Round 3 Chains 24, Residues 205, Estimated correctness of the model 65.8 % 3 chains (68 residues) have been docked in sequence Building loops using Loopy2018 24 chains (205 residues) following loop building 3 chains (68 residues) in sequence following loop building ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3835 restraints for refining 2235 atoms. 2748 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2735 (Rfree = 0.000) for 2235 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 17: After refmac, R = 0.2475 (Rfree = 0.000) for 2224 atoms. Found 10 (20 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.2348 (Rfree = 0.000) for 2217 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 19: After refmac, R = 0.2256 (Rfree = 0.000) for 2215 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 20: After refmac, R = 0.2235 (Rfree = 0.000) for 2208 atoms. Found 7 (17 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.98 2.68 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 61 residues added (18 deleted due to clashes), 2343 seeds are put forward Round 1: 208 peptides, 23 chains. Longest chain 21 peptides. Score 0.631 Round 2: 232 peptides, 19 chains. Longest chain 40 peptides. Score 0.738 Round 3: 222 peptides, 20 chains. Longest chain 29 peptides. Score 0.704 Round 4: 221 peptides, 19 chains. Longest chain 47 peptides. Score 0.713 Round 5: 220 peptides, 23 chains. Longest chain 25 peptides. Score 0.664 Taking the results from Round 2 Chains 20, Residues 213, Estimated correctness of the model 72.8 % 5 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 79 A 19 chains (215 residues) following loop building 4 chains (107 residues) in sequence following loop building ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3452 restraints for refining 2234 atoms. 2117 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2743 (Rfree = 0.000) for 2234 atoms. Found 18 (18 requested) and removed 31 (10 requested) atoms. Cycle 22: After refmac, R = 0.2562 (Rfree = 0.000) for 2212 atoms. Found 14 (17 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2497 (Rfree = 0.000) for 2206 atoms. Found 6 (16 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.2432 (Rfree = 0.000) for 2200 atoms. Found 5 (16 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2354 (Rfree = 0.000) for 2193 atoms. Found 6 (16 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.94 2.64 Search for helices and strands: 0 residues in 0 chains, 2263 seeds are put forward NCS extension: 38 residues added (35 deleted due to clashes), 2301 seeds are put forward Round 1: 209 peptides, 24 chains. Longest chain 20 peptides. Score 0.621 Round 2: 213 peptides, 23 chains. Longest chain 28 peptides. Score 0.645 Round 3: 216 peptides, 22 chains. Longest chain 28 peptides. Score 0.666 Round 4: 219 peptides, 22 chains. Longest chain 31 peptides. Score 0.674 Round 5: 210 peptides, 22 chains. Longest chain 28 peptides. Score 0.650 Taking the results from Round 4 Chains 24, Residues 197, Estimated correctness of the model 59.5 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 4152 restraints for refining 2235 atoms. 3189 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2597 (Rfree = 0.000) for 2235 atoms. Found 16 (16 requested) and removed 14 (10 requested) atoms. Cycle 27: After refmac, R = 0.2452 (Rfree = 0.000) for 2231 atoms. Found 12 (16 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2362 (Rfree = 0.000) for 2233 atoms. Found 7 (16 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2310 (Rfree = 0.000) for 2230 atoms. Found 2 (16 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 2220 atoms. Found 4 (15 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.96 2.66 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward NCS extension: 30 residues added (24 deleted due to clashes), 2308 seeds are put forward Round 1: 188 peptides, 19 chains. Longest chain 24 peptides. Score 0.627 Round 2: 203 peptides, 22 chains. Longest chain 34 peptides. Score 0.630 Round 3: 215 peptides, 21 chains. Longest chain 36 peptides. Score 0.675 Round 4: 212 peptides, 17 chains. Longest chain 50 peptides. Score 0.715 Round 5: 204 peptides, 23 chains. Longest chain 43 peptides. Score 0.620 Taking the results from Round 4 Chains 20, Residues 195, Estimated correctness of the model 68.3 % 3 chains (87 residues) have been docked in sequence Building loops using Loopy2018 20 chains (195 residues) following loop building 3 chains (87 residues) in sequence following loop building ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3782 restraints for refining 2235 atoms. 2672 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2572 (Rfree = 0.000) for 2235 atoms. Found 16 (16 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2427 (Rfree = 0.000) for 2225 atoms. Found 11 (16 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2303 (Rfree = 0.000) for 2222 atoms. Found 14 (14 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 2223 atoms. Found 6 (14 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2170 (Rfree = 0.000) for 2216 atoms. Found 2 (14 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.95 2.65 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 41 residues added (31 deleted due to clashes), 2300 seeds are put forward Round 1: 186 peptides, 21 chains. Longest chain 41 peptides. Score 0.593 Round 2: 206 peptides, 23 chains. Longest chain 37 peptides. Score 0.625 Round 3: 202 peptides, 22 chains. Longest chain 29 peptides. Score 0.627 Round 4: 216 peptides, 18 chains. Longest chain 44 peptides. Score 0.713 Round 5: 213 peptides, 18 chains. Longest chain 42 peptides. Score 0.706 Taking the results from Round 4 Chains 20, Residues 198, Estimated correctness of the model 67.9 % 4 chains (91 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 B and 62 B 19 chains (202 residues) following loop building 3 chains (95 residues) in sequence following loop building ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3606 restraints for refining 2235 atoms. 2432 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2570 (Rfree = 0.000) for 2235 atoms. Found 14 (14 requested) and removed 18 (10 requested) atoms. Cycle 37: After refmac, R = 0.2348 (Rfree = 0.000) for 2222 atoms. Found 12 (14 requested) and removed 15 (10 requested) atoms. Cycle 38: After refmac, R = 0.2252 (Rfree = 0.000) for 2213 atoms. Found 6 (13 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.2202 (Rfree = 0.000) for 2205 atoms. Found 4 (12 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2159 (Rfree = 0.000) for 2197 atoms. Found 8 (12 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.93 2.63 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 26 residues added (50 deleted due to clashes), 2285 seeds are put forward Round 1: 204 peptides, 21 chains. Longest chain 41 peptides. Score 0.646 Round 2: 227 peptides, 20 chains. Longest chain 59 peptides. Score 0.716 Round 3: 218 peptides, 22 chains. Longest chain 46 peptides. Score 0.671 Round 4: 229 peptides, 20 chains. Longest chain 37 peptides. Score 0.721 Round 5: 228 peptides, 19 chains. Longest chain 46 peptides. Score 0.729 Taking the results from Round 5 Chains 21, Residues 209, Estimated correctness of the model 71.1 % 2 chains (73 residues) have been docked in sequence Building loops using Loopy2018 21 chains (209 residues) following loop building 2 chains (73 residues) in sequence following loop building ------------------------------------------------------ 6969 reflections ( 99.80 % complete ) and 3796 restraints for refining 2235 atoms. 2655 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2664 (Rfree = 0.000) for 2235 atoms. Found 12 (12 requested) and removed 26 (10 requested) atoms. Cycle 42: After refmac, R = 0.2432 (Rfree = 0.000) for 2214 atoms. Found 9 (11 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.2374 (Rfree = 0.000) for 2207 atoms. Found 11 (11 requested) and removed 10 (9 requested) atoms. Cycle 44: After refmac, R = 0.2314 (Rfree = 0.000) for 2205 atoms. Found 6 (10 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2303 (Rfree = 0.000) for 2197 atoms. Found 4 (10 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.69 Search for helices and strands: 0 residues in 0 chains, 2262 seeds are put forward NCS extension: 17 residues added (34 deleted due to clashes), 2279 seeds are put forward Round 1: 190 peptides, 21 chains. Longest chain 29 peptides. Score 0.605 Round 2: 209 peptides, 20 chains. Longest chain 29 peptides. Score 0.672 Round 3: 209 peptides, 19 chains. Longest chain 31 peptides. Score 0.684 Round 4: 192 peptides, 19 chains. Longest chain 27 peptides. Score 0.639 Round 5: 208 peptides, 23 chains. Longest chain 22 peptides. Score 0.631 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 190, Estimated correctness of the model 61.7 % 3 chains (75 residues) have been docked in sequence Sequence coverage is 39 % Consider running further cycles of model building using 2glz-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 88 A and 90 A 19 chains (189 residues) following loop building 2 chains (76 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6969 reflections ( 99.80 % complete ) and 3877 restraints for refining 2235 atoms. 2801 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2604 (Rfree = 0.000) for 2235 atoms. Found 0 (10 requested) and removed 7 (10 requested) atoms. Cycle 47: After refmac, R = 0.2465 (Rfree = 0.000) for 2224 atoms. Found 0 (9 requested) and removed 2 (9 requested) atoms. Cycle 48: After refmac, R = 0.2381 (Rfree = 0.000) for 2217 atoms. Found 0 (9 requested) and removed 3 (9 requested) atoms. Cycle 49: After refmac, R = 0.2358 (Rfree = 0.000) for 2211 atoms. TimeTaking 36.45