Sun 23 Dec 22:22:43 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 1vjz-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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/1vjz-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 ============================================================ Sun 23 Dec 22:22:52 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/1vjz-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 315 and 0 Target number of residues in the AU: 315 Target solvent content: 0.5972 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.75 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: 61.607 3.400 Wilson plot Bfac: 51.07 6423 reflections ( 99.72 % complete ) and 0 restraints for refining 3030 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2767 (Rfree = 0.000) for 3030 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.03 2.80 Search for helices and strands: 0 residues in 0 chains, 3074 seeds are put forward Round 1: 186 peptides, 32 chains. Longest chain 11 peptides. Score 0.409 Round 2: 204 peptides, 32 chains. Longest chain 16 peptides. Score 0.474 Round 3: 207 peptides, 29 chains. Longest chain 23 peptides. Score 0.528 Round 4: 217 peptides, 32 chains. Longest chain 13 peptides. Score 0.517 Round 5: 222 peptides, 29 chains. Longest chain 20 peptides. Score 0.574 Taking the results from Round 5 Chains 29, Residues 193, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5333 restraints for refining 2481 atoms. 4590 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2503 (Rfree = 0.000) for 2481 atoms. Found 15 (18 requested) and removed 15 (9 requested) atoms. Cycle 2: After refmac, R = 0.2438 (Rfree = 0.000) for 2464 atoms. Found 5 (18 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2417 (Rfree = 0.000) for 2453 atoms. Found 9 (18 requested) and removed 21 (9 requested) atoms. Cycle 4: After refmac, R = 0.2351 (Rfree = 0.000) for 2432 atoms. Found 1 (18 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2273 (Rfree = 0.000) for 2421 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.83 Search for helices and strands: 0 residues in 0 chains, 2533 seeds are put forward Round 1: 206 peptides, 31 chains. Longest chain 15 peptides. Score 0.496 Round 2: 216 peptides, 30 chains. Longest chain 15 peptides. Score 0.542 Round 3: 219 peptides, 30 chains. Longest chain 28 peptides. Score 0.551 Round 4: 223 peptides, 31 chains. Longest chain 16 peptides. Score 0.550 Round 5: 229 peptides, 29 chains. Longest chain 18 peptides. Score 0.594 Taking the results from Round 5 Chains 29, Residues 200, Estimated correctness of the model 26.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5435 restraints for refining 2481 atoms. 4664 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2587 (Rfree = 0.000) for 2481 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 7: After refmac, R = 0.2390 (Rfree = 0.000) for 2474 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 8: After refmac, R = 0.2364 (Rfree = 0.000) for 2467 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.2387 (Rfree = 0.000) for 2461 atoms. Found 6 (18 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2337 (Rfree = 0.000) for 2448 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.80 Search for helices and strands: 0 residues in 0 chains, 2530 seeds are put forward Round 1: 221 peptides, 31 chains. Longest chain 23 peptides. Score 0.544 Round 2: 224 peptides, 29 chains. Longest chain 28 peptides. Score 0.580 Round 3: 242 peptides, 30 chains. Longest chain 20 peptides. Score 0.618 Round 4: 239 peptides, 30 chains. Longest chain 19 peptides. Score 0.610 Round 5: 242 peptides, 27 chains. Longest chain 23 peptides. Score 0.653 Taking the results from Round 5 Chains 28, Residues 215, Estimated correctness of the model 45.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 4866 restraints for refining 2481 atoms. 3860 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2653 (Rfree = 0.000) for 2481 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 12: After refmac, R = 0.2432 (Rfree = 0.000) for 2464 atoms. Found 14 (18 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2333 (Rfree = 0.000) for 2465 atoms. Found 8 (18 requested) and removed 19 (9 requested) atoms. Cycle 14: After refmac, R = 0.2275 (Rfree = 0.000) for 2449 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 2444 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 2.85 Search for helices and strands: 0 residues in 0 chains, 2520 seeds are put forward Round 1: 209 peptides, 29 chains. Longest chain 17 peptides. Score 0.534 Round 2: 211 peptides, 25 chains. Longest chain 19 peptides. Score 0.595 Round 3: 227 peptides, 28 chains. Longest chain 16 peptides. Score 0.601 Round 4: 232 peptides, 24 chains. Longest chain 23 peptides. Score 0.663 Round 5: 222 peptides, 28 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Chains 24, Residues 208, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5285 restraints for refining 2480 atoms. 4477 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2563 (Rfree = 0.000) for 2480 atoms. Found 17 (18 requested) and removed 19 (9 requested) atoms. Cycle 17: After refmac, R = 0.2300 (Rfree = 0.000) for 2475 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2243 (Rfree = 0.000) for 2468 atoms. Found 3 (18 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2203 (Rfree = 0.000) for 2459 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2186 (Rfree = 0.000) for 2452 atoms. Found 2 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.83 Search for helices and strands: 0 residues in 0 chains, 2518 seeds are put forward Round 1: 192 peptides, 27 chains. Longest chain 12 peptides. Score 0.508 Round 2: 213 peptides, 27 chains. Longest chain 17 peptides. Score 0.574 Round 3: 223 peptides, 24 chains. Longest chain 23 peptides. Score 0.640 Round 4: 215 peptides, 27 chains. Longest chain 15 peptides. Score 0.580 Round 5: 208 peptides, 24 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 3 Chains 25, Residues 199, Estimated correctness of the model 41.2 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5139 restraints for refining 2481 atoms. 4303 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2522 (Rfree = 0.000) for 2481 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2411 (Rfree = 0.000) for 2468 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 23: After refmac, R = 0.2396 (Rfree = 0.000) for 2458 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2379 (Rfree = 0.000) for 2448 atoms. Found 2 (18 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2358 (Rfree = 0.000) for 2437 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.82 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward Round 1: 189 peptides, 28 chains. Longest chain 17 peptides. Score 0.483 Round 2: 217 peptides, 30 chains. Longest chain 17 peptides. Score 0.545 Round 3: 229 peptides, 28 chains. Longest chain 20 peptides. Score 0.607 Round 4: 213 peptides, 29 chains. Longest chain 21 peptides. Score 0.547 Round 5: 213 peptides, 27 chains. Longest chain 16 peptides. Score 0.574 Taking the results from Round 3 Chains 29, Residues 201, Estimated correctness of the model 30.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5146 restraints for refining 2481 atoms. 4281 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2631 (Rfree = 0.000) for 2481 atoms. Found 14 (18 requested) and removed 24 (9 requested) atoms. Cycle 27: After refmac, R = 0.2440 (Rfree = 0.000) for 2462 atoms. Found 7 (18 requested) and removed 21 (9 requested) atoms. Cycle 28: After refmac, R = 0.2380 (Rfree = 0.000) for 2443 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2324 (Rfree = 0.000) for 2434 atoms. Found 4 (18 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2304 (Rfree = 0.000) for 2423 atoms. Found 3 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.77 Search for helices and strands: 0 residues in 0 chains, 2459 seeds are put forward Round 1: 182 peptides, 30 chains. Longest chain 15 peptides. Score 0.427 Round 2: 205 peptides, 28 chains. Longest chain 19 peptides. Score 0.536 Round 3: 211 peptides, 26 chains. Longest chain 24 peptides. Score 0.581 Round 4: 207 peptides, 26 chains. Longest chain 24 peptides. Score 0.570 Round 5: 199 peptides, 26 chains. Longest chain 21 peptides. Score 0.545 Taking the results from Round 3 Chains 26, Residues 185, Estimated correctness of the model 22.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 5340 restraints for refining 2481 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2369 (Rfree = 0.000) for 2481 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 32: After refmac, R = 0.2301 (Rfree = 0.000) for 2473 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2263 (Rfree = 0.000) for 2470 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 2465 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.2146 (Rfree = 0.000) for 2455 atoms. Found 1 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 2.79 Search for helices and strands: 0 residues in 0 chains, 2513 seeds are put forward Round 1: 179 peptides, 28 chains. Longest chain 14 peptides. Score 0.447 Round 2: 196 peptides, 24 chains. Longest chain 25 peptides. Score 0.564 Round 3: 195 peptides, 27 chains. Longest chain 16 peptides. Score 0.518 Round 4: 196 peptides, 22 chains. Longest chain 24 peptides. Score 0.591 Round 5: 194 peptides, 22 chains. Longest chain 20 peptides. Score 0.585 Taking the results from Round 4 Chains 22, Residues 174, Estimated correctness of the model 25.7 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 4995 restraints for refining 2481 atoms. 4188 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2402 (Rfree = 0.000) for 2481 atoms. Found 13 (18 requested) and removed 18 (9 requested) atoms. Cycle 37: After refmac, R = 0.2281 (Rfree = 0.000) for 2470 atoms. Found 4 (18 requested) and removed 14 (9 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 2459 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.2205 (Rfree = 0.000) for 2449 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2122 (Rfree = 0.000) for 2442 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 2.78 Search for helices and strands: 0 residues in 0 chains, 2501 seeds are put forward Round 1: 177 peptides, 25 chains. Longest chain 20 peptides. Score 0.487 Round 2: 188 peptides, 24 chains. Longest chain 16 peptides. Score 0.539 Round 3: 188 peptides, 24 chains. Longest chain 35 peptides. Score 0.539 Round 4: 198 peptides, 22 chains. Longest chain 23 peptides. Score 0.597 Round 5: 192 peptides, 23 chains. Longest chain 20 peptides. Score 0.566 Taking the results from Round 4 Chains 24, Residues 176, Estimated correctness of the model 27.7 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6423 reflections ( 99.72 % complete ) and 4669 restraints for refining 2481 atoms. 3750 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2367 (Rfree = 0.000) for 2481 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 42: After refmac, R = 0.2212 (Rfree = 0.000) for 2480 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.2140 (Rfree = 0.000) for 2476 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2066 (Rfree = 0.000) for 2470 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 2466 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 2.81 Search for helices and strands: 0 residues in 0 chains, 2527 seeds are put forward Round 1: 170 peptides, 29 chains. Longest chain 14 peptides. Score 0.398 Round 2: 201 peptides, 27 chains. Longest chain 23 peptides. Score 0.537 Round 3: 207 peptides, 30 chains. Longest chain 14 peptides. Score 0.513 Round 4: 203 peptides, 29 chains. Longest chain 20 peptides. Score 0.515 Round 5: 192 peptides, 27 chains. Longest chain 14 peptides. Score 0.508 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 174, Estimated correctness of the model 6.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vjz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6423 reflections ( 99.72 % complete ) and 5283 restraints for refining 2481 atoms. 4614 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2173 (Rfree = 0.000) for 2481 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2102 (Rfree = 0.000) for 2469 atoms. Found 0 (18 requested) and removed 6 (9 requested) atoms. Cycle 48: After refmac, R = 0.2099 (Rfree = 0.000) for 2460 atoms. Found 0 (18 requested) and removed 2 (9 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 2458 atoms. TimeTaking 49.17