null 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 1zy9-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.8-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/1zy9-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.8-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/1zy9-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.8-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 585 and 0 Target number of residues in the AU: 585 Target solvent content: 0.6336 Checking the provided sequence file Detected sequence length: 564 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 564 Adjusted target solvent content: 0.65 Input MTZ file: 1zy9-3.8-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: 20 Cell parameters: 121.755 160.844 88.238 90.000 90.000 90.000 Input sequence file: 1zy9-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4512 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: 97.078 3.800 Wilson plot Bfac: 68.35 8462 reflections ( 95.50 % complete ) and 0 restraints for refining 4967 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3190 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3092 (Rfree = 0.000) for 4967 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 5049 seeds are put forward Round 1: 266 peptides, 50 chains. Longest chain 12 peptides. Score 0.317 Round 2: 338 peptides, 47 chains. Longest chain 18 peptides. Score 0.478 Round 3: 365 peptides, 45 chains. Longest chain 27 peptides. Score 0.538 Round 4: 367 peptides, 40 chains. Longest chain 36 peptides. Score 0.577 Round 5: 374 peptides, 41 chains. Longest chain 24 peptides. Score 0.580 Taking the results from Round 5 Chains 45, Residues 333, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8888 restraints for refining 4080 atoms. 7506 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2674 (Rfree = 0.000) for 4080 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 2: After refmac, R = 0.2492 (Rfree = 0.000) for 3984 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 3: After refmac, R = 0.2309 (Rfree = 0.000) for 3949 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. Cycle 4: After refmac, R = 0.2137 (Rfree = 0.000) for 3912 atoms. Found 18 (21 requested) and removed 19 (10 requested) atoms. Cycle 5: After refmac, R = 0.2162 (Rfree = 0.000) for 3899 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.82 Search for helices and strands: 0 residues in 0 chains, 4025 seeds are put forward Round 1: 345 peptides, 47 chains. Longest chain 14 peptides. Score 0.490 Round 2: 373 peptides, 40 chains. Longest chain 24 peptides. Score 0.585 Round 3: 388 peptides, 41 chains. Longest chain 25 peptides. Score 0.600 Round 4: 391 peptides, 44 chains. Longest chain 25 peptides. Score 0.584 Round 5: 389 peptides, 36 chains. Longest chain 28 peptides. Score 0.634 Taking the results from Round 5 Chains 38, Residues 353, Estimated correctness of the model 14.1 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8533 restraints for refining 4079 atoms. 7019 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2485 (Rfree = 0.000) for 4079 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 7: After refmac, R = 0.2203 (Rfree = 0.000) for 4025 atoms. Found 14 (22 requested) and removed 19 (11 requested) atoms. Cycle 8: After refmac, R = 0.2111 (Rfree = 0.000) for 4006 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 9: After refmac, R = 0.2080 (Rfree = 0.000) for 3988 atoms. Found 8 (21 requested) and removed 18 (10 requested) atoms. Cycle 10: After refmac, R = 0.2084 (Rfree = 0.000) for 3974 atoms. Found 10 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 2.83 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward Round 1: 370 peptides, 50 chains. Longest chain 21 peptides. Score 0.509 Round 2: 393 peptides, 44 chains. Longest chain 27 peptides. Score 0.587 Round 3: 370 peptides, 40 chains. Longest chain 26 peptides. Score 0.581 Round 4: 394 peptides, 42 chains. Longest chain 27 peptides. Score 0.602 Round 5: 386 peptides, 40 chains. Longest chain 36 peptides. Score 0.604 Taking the results from Round 5 Chains 43, Residues 346, Estimated correctness of the model 0.7 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8165 restraints for refining 4080 atoms. 6547 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2632 (Rfree = 0.000) for 4080 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 12: After refmac, R = 0.2614 (Rfree = 0.000) for 4057 atoms. Found 15 (22 requested) and removed 20 (11 requested) atoms. Cycle 13: After refmac, R = 0.2787 (Rfree = 0.000) for 4045 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 14: After refmac, R = 0.2696 (Rfree = 0.000) for 4035 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 15: After refmac, R = 0.2510 (Rfree = 0.000) for 4016 atoms. Found 14 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.82 Search for helices and strands: 0 residues in 0 chains, 4112 seeds are put forward Round 1: 333 peptides, 50 chains. Longest chain 22 peptides. Score 0.446 Round 2: 361 peptides, 44 chains. Longest chain 27 peptides. Score 0.539 Round 3: 363 peptides, 43 chains. Longest chain 26 peptides. Score 0.549 Round 4: 370 peptides, 41 chains. Longest chain 27 peptides. Score 0.574 Round 5: 381 peptides, 42 chains. Longest chain 25 peptides. Score 0.583 Taking the results from Round 5 Chains 47, Residues 339, Estimated correctness of the model 0.0 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8226 restraints for refining 4080 atoms. 6632 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2600 (Rfree = 0.000) for 4080 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 17: After refmac, R = 0.2410 (Rfree = 0.000) for 4031 atoms. Found 19 (22 requested) and removed 25 (11 requested) atoms. Cycle 18: After refmac, R = 0.2240 (Rfree = 0.000) for 4005 atoms. Found 7 (22 requested) and removed 18 (11 requested) atoms. Cycle 19: After refmac, R = 0.2245 (Rfree = 0.000) for 3975 atoms. Found 11 (21 requested) and removed 14 (10 requested) atoms. Cycle 20: After refmac, R = 0.2211 (Rfree = 0.000) for 3965 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 4082 seeds are put forward Round 1: 353 peptides, 52 chains. Longest chain 18 peptides. Score 0.466 Round 2: 355 peptides, 42 chains. Longest chain 36 peptides. Score 0.544 Round 3: 363 peptides, 47 chains. Longest chain 25 peptides. Score 0.520 Round 4: 375 peptides, 46 chains. Longest chain 20 peptides. Score 0.546 Round 5: 377 peptides, 45 chains. Longest chain 21 peptides. Score 0.557 Taking the results from Round 5 Chains 46, Residues 332, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8642 restraints for refining 4081 atoms. 7218 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2525 (Rfree = 0.000) for 4081 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 22: After refmac, R = 0.2408 (Rfree = 0.000) for 4035 atoms. Found 20 (22 requested) and removed 17 (11 requested) atoms. Cycle 23: After refmac, R = 0.2340 (Rfree = 0.000) for 4014 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. Cycle 24: After refmac, R = 0.2148 (Rfree = 0.000) for 3997 atoms. Found 9 (22 requested) and removed 17 (11 requested) atoms. Cycle 25: After refmac, R = 0.2359 (Rfree = 0.000) for 3976 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.82 Search for helices and strands: 0 residues in 0 chains, 4104 seeds are put forward Round 1: 324 peptides, 50 chains. Longest chain 19 peptides. Score 0.430 Round 2: 347 peptides, 42 chains. Longest chain 26 peptides. Score 0.531 Round 3: 346 peptides, 45 chains. Longest chain 21 peptides. Score 0.507 Round 4: 372 peptides, 49 chains. Longest chain 36 peptides. Score 0.520 Round 5: 356 peptides, 49 chains. Longest chain 25 peptides. Score 0.494 Taking the results from Round 2 Chains 43, Residues 305, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8721 restraints for refining 4081 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2785 (Rfree = 0.000) for 4081 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 27: After refmac, R = 0.2546 (Rfree = 0.000) for 4040 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 28: After refmac, R = 0.2614 (Rfree = 0.000) for 4029 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 29: After refmac, R = 0.2225 (Rfree = 0.000) for 4016 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. Cycle 30: After refmac, R = 0.2545 (Rfree = 0.000) for 3997 atoms. Found 22 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 4101 seeds are put forward Round 1: 311 peptides, 53 chains. Longest chain 14 peptides. Score 0.381 Round 2: 339 peptides, 50 chains. Longest chain 16 peptides. Score 0.457 Round 3: 357 peptides, 43 chains. Longest chain 37 peptides. Score 0.540 Round 4: 354 peptides, 46 chains. Longest chain 22 peptides. Score 0.513 Round 5: 320 peptides, 42 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 3 Chains 47, Residues 314, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8850 restraints for refining 4079 atoms. 7565 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2666 (Rfree = 0.000) for 4079 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 32: After refmac, R = 0.2403 (Rfree = 0.000) for 4026 atoms. Found 15 (22 requested) and removed 20 (11 requested) atoms. Cycle 33: After refmac, R = 0.2336 (Rfree = 0.000) for 4000 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 34: After refmac, R = 0.2152 (Rfree = 0.000) for 3991 atoms. Found 3 (22 requested) and removed 17 (11 requested) atoms. Cycle 35: After refmac, R = 0.2163 (Rfree = 0.000) for 3966 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 4065 seeds are put forward Round 1: 317 peptides, 49 chains. Longest chain 17 peptides. Score 0.425 Round 2: 346 peptides, 47 chains. Longest chain 21 peptides. Score 0.492 Round 3: 341 peptides, 47 chains. Longest chain 17 peptides. Score 0.484 Round 4: 335 peptides, 39 chains. Longest chain 27 peptides. Score 0.534 Round 5: 352 peptides, 42 chains. Longest chain 26 peptides. Score 0.539 Taking the results from Round 5 Chains 42, Residues 310, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8736 restraints for refining 4081 atoms. 7430 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2645 (Rfree = 0.000) for 4081 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 37: After refmac, R = 0.2585 (Rfree = 0.000) for 4035 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 38: After refmac, R = 0.2524 (Rfree = 0.000) for 4016 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.2562 (Rfree = 0.000) for 4006 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.2541 (Rfree = 0.000) for 3993 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 4085 seeds are put forward Round 1: 288 peptides, 50 chains. Longest chain 13 peptides. Score 0.361 Round 2: 317 peptides, 42 chains. Longest chain 19 peptides. Score 0.481 Round 3: 354 peptides, 49 chains. Longest chain 20 peptides. Score 0.490 Round 4: 340 peptides, 46 chains. Longest chain 20 peptides. Score 0.490 Round 5: 331 peptides, 41 chains. Longest chain 29 peptides. Score 0.513 Taking the results from Round 5 Chains 45, Residues 290, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8462 reflections ( 95.50 % complete ) and 8979 restraints for refining 4081 atoms. 7779 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3191 (Rfree = 0.000) for 4081 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 42: After refmac, R = 0.2730 (Rfree = 0.000) for 4056 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 43: After refmac, R = 0.2425 (Rfree = 0.000) for 4043 atoms. Found 19 (22 requested) and removed 18 (11 requested) atoms. Cycle 44: After refmac, R = 0.2412 (Rfree = 0.000) for 4022 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.2411 (Rfree = 0.000) for 4019 atoms. Found 14 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.82 Search for helices and strands: 0 residues in 0 chains, 4116 seeds are put forward Round 1: 269 peptides, 52 chains. Longest chain 10 peptides. Score 0.305 Round 2: 301 peptides, 44 chains. Longest chain 19 peptides. Score 0.437 Round 3: 324 peptides, 48 chains. Longest chain 24 peptides. Score 0.446 Round 4: 325 peptides, 48 chains. Longest chain 21 peptides. Score 0.448 Round 5: 332 peptides, 45 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 287, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1zy9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8462 reflections ( 95.50 % complete ) and 9133 restraints for refining 4081 atoms. 7989 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2956 (Rfree = 0.000) for 4081 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2768 (Rfree = 0.000) for 4029 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2396 (Rfree = 0.000) for 4003 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2280 (Rfree = 0.000) for 3972 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:39:25 GMT 2018 Job finished. TimeTaking 71.47 Used memory is bytes: 2900288