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 2fno-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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/2fno-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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/2fno-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.2-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 412 and 0 Target number of residues in the AU: 412 Target solvent content: 0.6203 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.2-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3968 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 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: 106.006 3.200 Wilson plot Bfac: 61.57 9774 reflections ( 99.42 % complete ) and 0 restraints for refining 4422 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3132 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3046 (Rfree = 0.000) for 4422 atoms. Found 39 (39 requested) and removed 40 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 4529 seeds are put forward NCS extension: 0 residues added, 4529 seeds are put forward Round 1: 217 peptides, 42 chains. Longest chain 10 peptides. Score 0.323 Round 2: 264 peptides, 39 chains. Longest chain 15 peptides. Score 0.486 Round 3: 299 peptides, 41 chains. Longest chain 22 peptides. Score 0.547 Round 4: 315 peptides, 46 chains. Longest chain 17 peptides. Score 0.533 Round 5: 321 peptides, 46 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 5 Chains 46, Residues 275, Estimated correctness of the model 26.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7884 restraints for refining 3620 atoms. 6773 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2788 (Rfree = 0.000) for 3620 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 2: After refmac, R = 0.2632 (Rfree = 0.000) for 3582 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2440 (Rfree = 0.000) for 3570 atoms. Found 30 (32 requested) and removed 22 (16 requested) atoms. Cycle 4: After refmac, R = 0.2460 (Rfree = 0.000) for 3572 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 5: After refmac, R = 0.2449 (Rfree = 0.000) for 3568 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3742 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3760 seeds are put forward Round 1: 287 peptides, 43 chains. Longest chain 18 peptides. Score 0.499 Round 2: 298 peptides, 39 chains. Longest chain 31 peptides. Score 0.565 Round 3: 310 peptides, 36 chains. Longest chain 34 peptides. Score 0.618 Round 4: 314 peptides, 39 chains. Longest chain 37 peptides. Score 0.598 Round 5: 322 peptides, 37 chains. Longest chain 32 peptides. Score 0.632 Taking the results from Round 5 Chains 39, Residues 285, Estimated correctness of the model 49.4 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7485 restraints for refining 3623 atoms. 6214 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2483 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2242 (Rfree = 0.000) for 3612 atoms. Found 20 (32 requested) and removed 23 (16 requested) atoms. Cycle 8: After refmac, R = 0.2123 (Rfree = 0.000) for 3603 atoms. Found 17 (32 requested) and removed 17 (16 requested) atoms. Cycle 9: After refmac, R = 0.2014 (Rfree = 0.000) for 3601 atoms. Found 6 (32 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.1979 (Rfree = 0.000) for 3584 atoms. Found 4 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 3722 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3746 seeds are put forward Round 1: 299 peptides, 41 chains. Longest chain 27 peptides. Score 0.547 Round 2: 319 peptides, 41 chains. Longest chain 19 peptides. Score 0.590 Round 3: 317 peptides, 38 chains. Longest chain 17 peptides. Score 0.614 Round 4: 325 peptides, 40 chains. Longest chain 36 peptides. Score 0.611 Round 5: 314 peptides, 37 chains. Longest chain 32 peptides. Score 0.617 Taking the results from Round 5 Chains 38, Residues 277, Estimated correctness of the model 45.6 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9774 reflections ( 99.42 % complete ) and 7764 restraints for refining 3623 atoms. 6586 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2354 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 12: After refmac, R = 0.2439 (Rfree = 0.000) for 3616 atoms. Found 26 (32 requested) and removed 22 (16 requested) atoms. Cycle 13: After refmac, R = 0.2239 (Rfree = 0.000) for 3609 atoms. Found 22 (32 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2174 (Rfree = 0.000) for 3607 atoms. Found 17 (32 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.2086 (Rfree = 0.000) for 3606 atoms. Found 7 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 3736 seeds are put forward NCS extension: 43 residues added (2 deleted due to clashes), 3779 seeds are put forward Round 1: 288 peptides, 44 chains. Longest chain 17 peptides. Score 0.491 Round 2: 322 peptides, 38 chains. Longest chain 35 peptides. Score 0.623 Round 3: 319 peptides, 35 chains. Longest chain 20 peptides. Score 0.644 Round 4: 298 peptides, 40 chains. Longest chain 18 peptides. Score 0.555 Round 5: 306 peptides, 35 chains. Longest chain 25 peptides. Score 0.619 Taking the results from Round 3 Chains 35, Residues 284, Estimated correctness of the model 52.4 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7925 restraints for refining 3623 atoms. 6803 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2351 (Rfree = 0.000) for 3623 atoms. Found 28 (32 requested) and removed 23 (16 requested) atoms. Cycle 17: After refmac, R = 0.2271 (Rfree = 0.000) for 3623 atoms. Found 22 (32 requested) and removed 16 (16 requested) atoms. Cycle 18: After refmac, R = 0.2208 (Rfree = 0.000) for 3617 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2019 (Rfree = 0.000) for 3619 atoms. Found 23 (32 requested) and removed 18 (16 requested) atoms. Cycle 20: After refmac, R = 0.1952 (Rfree = 0.000) for 3618 atoms. Found 10 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3740 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3750 seeds are put forward Round 1: 249 peptides, 43 chains. Longest chain 11 peptides. Score 0.401 Round 2: 291 peptides, 42 chains. Longest chain 17 peptides. Score 0.519 Round 3: 311 peptides, 39 chains. Longest chain 16 peptides. Score 0.592 Round 4: 317 peptides, 43 chains. Longest chain 17 peptides. Score 0.567 Round 5: 310 peptides, 42 chains. Longest chain 18 peptides. Score 0.562 Taking the results from Round 3 Chains 41, Residues 272, Estimated correctness of the model 38.9 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7979 restraints for refining 3622 atoms. 6893 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2477 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 22: After refmac, R = 0.2423 (Rfree = 0.000) for 3621 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 23: After refmac, R = 0.2248 (Rfree = 0.000) for 3604 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 24: After refmac, R = 0.2070 (Rfree = 0.000) for 3603 atoms. Found 25 (32 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2158 (Rfree = 0.000) for 3603 atoms. Found 28 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.93 Search for helices and strands: 0 residues in 0 chains, 3733 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3748 seeds are put forward Round 1: 283 peptides, 48 chains. Longest chain 13 peptides. Score 0.435 Round 2: 309 peptides, 45 chains. Longest chain 19 peptides. Score 0.530 Round 3: 317 peptides, 47 chains. Longest chain 30 peptides. Score 0.528 Round 4: 301 peptides, 44 chains. Longest chain 14 peptides. Score 0.521 Round 5: 310 peptides, 43 chains. Longest chain 15 peptides. Score 0.552 Taking the results from Round 5 Chains 43, Residues 267, Estimated correctness of the model 27.5 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8017 restraints for refining 3623 atoms. 6953 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2485 (Rfree = 0.000) for 3623 atoms. Found 24 (32 requested) and removed 25 (16 requested) atoms. Cycle 27: After refmac, R = 0.2271 (Rfree = 0.000) for 3616 atoms. Found 30 (32 requested) and removed 21 (16 requested) atoms. Cycle 28: After refmac, R = 0.2204 (Rfree = 0.000) for 3624 atoms. Found 24 (32 requested) and removed 20 (16 requested) atoms. Cycle 29: After refmac, R = 0.2253 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2071 (Rfree = 0.000) for 3632 atoms. Found 24 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3772 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3789 seeds are put forward Round 1: 243 peptides, 41 chains. Longest chain 15 peptides. Score 0.409 Round 2: 267 peptides, 42 chains. Longest chain 17 peptides. Score 0.460 Round 3: 283 peptides, 43 chains. Longest chain 15 peptides. Score 0.489 Round 4: 287 peptides, 42 chains. Longest chain 19 peptides. Score 0.509 Round 5: 284 peptides, 37 chains. Longest chain 20 peptides. Score 0.554 Taking the results from Round 5 Chains 38, Residues 247, Estimated correctness of the model 28.1 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8026 restraints for refining 3623 atoms. 7009 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2680 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2337 (Rfree = 0.000) for 3606 atoms. Found 26 (32 requested) and removed 19 (16 requested) atoms. Cycle 33: After refmac, R = 0.2346 (Rfree = 0.000) for 3603 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 34: After refmac, R = 0.2267 (Rfree = 0.000) for 3611 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.2259 (Rfree = 0.000) for 3614 atoms. Found 27 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 3787 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 3802 seeds are put forward Round 1: 233 peptides, 42 chains. Longest chain 12 peptides. Score 0.369 Round 2: 267 peptides, 38 chains. Longest chain 17 peptides. Score 0.504 Round 3: 272 peptides, 40 chains. Longest chain 19 peptides. Score 0.494 Round 4: 254 peptides, 37 chains. Longest chain 20 peptides. Score 0.483 Round 5: 260 peptides, 38 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 2 Chains 38, Residues 229, Estimated correctness of the model 12.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 8270 restraints for refining 3623 atoms. 7348 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2539 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 3628 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 38: After refmac, R = 0.2284 (Rfree = 0.000) for 3636 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.2226 (Rfree = 0.000) for 3643 atoms. Found 25 (32 requested) and removed 19 (16 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2263 (Rfree = 0.000) for 3644 atoms. Found 25 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3779 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3801 seeds are put forward Round 1: 221 peptides, 42 chains. Longest chain 13 peptides. Score 0.334 Round 2: 270 peptides, 40 chains. Longest chain 28 peptides. Score 0.490 Round 3: 264 peptides, 38 chains. Longest chain 20 peptides. Score 0.496 Round 4: 264 peptides, 40 chains. Longest chain 17 peptides. Score 0.475 Round 5: 262 peptides, 34 chains. Longest chain 25 peptides. Score 0.534 Taking the results from Round 5 Chains 36, Residues 228, Estimated correctness of the model 22.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9774 reflections ( 99.42 % complete ) and 7958 restraints for refining 3623 atoms. 7005 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2475 (Rfree = 0.000) for 3623 atoms. Found 32 (32 requested) and removed 18 (16 requested) atoms. Cycle 42: After refmac, R = 0.2554 (Rfree = 0.000) for 3631 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 43: After refmac, R = 0.2382 (Rfree = 0.000) for 3640 atoms. Found 16 (32 requested) and removed 23 (16 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 3629 atoms. Found 16 (32 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.2429 (Rfree = 0.000) for 3621 atoms. Found 19 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3799 seeds are put forward Round 1: 239 peptides, 40 chains. Longest chain 16 peptides. Score 0.409 Round 2: 249 peptides, 39 chains. Longest chain 15 peptides. Score 0.448 Round 3: 246 peptides, 38 chains. Longest chain 15 peptides. Score 0.451 Round 4: 249 peptides, 37 chains. Longest chain 20 peptides. Score 0.470 Round 5: 243 peptides, 35 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 208, Estimated correctness of the model 4.1 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 9774 reflections ( 99.42 % complete ) and 8345 restraints for refining 3623 atoms. 7538 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2467 (Rfree = 0.000) for 3623 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2269 (Rfree = 0.000) for 3596 atoms. Found 0 (32 requested) and removed 6 (16 requested) atoms. Cycle 48: After refmac, R = 0.2233 (Rfree = 0.000) for 3585 atoms. Found 0 (32 requested) and removed 4 (16 requested) atoms. Cycle 49: After refmac, R = 0.2218 (Rfree = 0.000) for 3578 atoms. Found 0 (32 requested) and removed 2 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:34:19 GMT 2018 Job finished. TimeTaking 66.37