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 1zy9-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-4.0-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/1zy9-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-4.0-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 19:28:07 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/1zy9-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-4.0-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 567 and 0 Target number of residues in the AU: 567 Target solvent content: 0.6448 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: 1zy9-4.0-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: 1zy9-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4512 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 Loops will be built when appropriate and at the last cycle Resolution range: 97.078 4.000 Wilson plot Bfac: 74.64 7253 reflections ( 95.17 % complete ) and 0 restraints for refining 4980 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3196 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3413 (Rfree = 0.000) for 4980 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 5030 seeds are put forward Round 1: 231 peptides, 44 chains. Longest chain 9 peptides. Score 0.297 Round 2: 291 peptides, 44 chains. Longest chain 17 peptides. Score 0.418 Round 3: 312 peptides, 43 chains. Longest chain 19 peptides. Score 0.465 Round 4: 334 peptides, 41 chains. Longest chain 18 peptides. Score 0.518 Round 5: 334 peptides, 47 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 4 Chains 45, Residues 293, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 8838 restraints for refining 4074 atoms. 7573 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2961 (Rfree = 0.000) for 4074 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 2: After refmac, R = 0.2694 (Rfree = 0.000) for 3983 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 3: After refmac, R = 0.2631 (Rfree = 0.000) for 3922 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 4: After refmac, R = 0.2612 (Rfree = 0.000) for 3869 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 5: After refmac, R = 0.2447 (Rfree = 0.000) for 3819 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3949 seeds are put forward Round 1: 305 peptides, 50 chains. Longest chain 16 peptides. Score 0.394 Round 2: 329 peptides, 40 chains. Longest chain 24 peptides. Score 0.517 Round 3: 330 peptides, 38 chains. Longest chain 29 peptides. Score 0.534 Round 4: 330 peptides, 42 chains. Longest chain 20 peptides. Score 0.503 Round 5: 354 peptides, 37 chains. Longest chain 30 peptides. Score 0.578 Taking the results from Round 5 Chains 40, Residues 317, Estimated correctness of the model 0.0 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 8566 restraints for refining 4073 atoms. 7142 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2504 (Rfree = 0.000) for 4073 atoms. Found 16 (19 requested) and removed 30 (9 requested) atoms. Cycle 7: After refmac, R = 0.2297 (Rfree = 0.000) for 3987 atoms. Found 13 (19 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.2221 (Rfree = 0.000) for 3950 atoms. Found 9 (18 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2169 (Rfree = 0.000) for 3926 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2155 (Rfree = 0.000) for 3911 atoms. Found 7 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 4026 seeds are put forward Round 1: 335 peptides, 50 chains. Longest chain 21 peptides. Score 0.450 Round 2: 341 peptides, 45 chains. Longest chain 17 peptides. Score 0.499 Round 3: 352 peptides, 40 chains. Longest chain 23 peptides. Score 0.554 Round 4: 363 peptides, 42 chains. Longest chain 23 peptides. Score 0.556 Round 5: 350 peptides, 35 chains. Longest chain 28 peptides. Score 0.586 Taking the results from Round 5 Chains 37, Residues 315, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 8811 restraints for refining 4075 atoms. 7464 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2829 (Rfree = 0.000) for 4075 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.2726 (Rfree = 0.000) for 4045 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2520 (Rfree = 0.000) for 4024 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 14: After refmac, R = 0.2643 (Rfree = 0.000) for 4010 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2659 (Rfree = 0.000) for 3992 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 2.95 Search for helices and strands: 0 residues in 0 chains, 4081 seeds are put forward Round 1: 305 peptides, 48 chains. Longest chain 14 peptides. Score 0.411 Round 2: 332 peptides, 46 chains. Longest chain 28 peptides. Score 0.476 Round 3: 323 peptides, 42 chains. Longest chain 20 peptides. Score 0.492 Round 4: 334 peptides, 42 chains. Longest chain 20 peptides. Score 0.510 Round 5: 343 peptides, 44 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 5 Chains 47, Residues 299, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 8926 restraints for refining 4075 atoms. 7668 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2740 (Rfree = 0.000) for 4075 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 17: After refmac, R = 0.2498 (Rfree = 0.000) for 4041 atoms. Found 16 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.2389 (Rfree = 0.000) for 4027 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 19: After refmac, R = 0.2441 (Rfree = 0.000) for 4015 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2411 (Rfree = 0.000) for 4012 atoms. Found 2 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.61 2.94 Search for helices and strands: 0 residues in 0 chains, 4112 seeds are put forward Round 1: 303 peptides, 50 chains. Longest chain 19 peptides. Score 0.391 Round 2: 317 peptides, 44 chains. Longest chain 19 peptides. Score 0.465 Round 3: 322 peptides, 45 chains. Longest chain 17 peptides. Score 0.466 Round 4: 306 peptides, 42 chains. Longest chain 18 peptides. Score 0.462 Round 5: 330 peptides, 43 chains. Longest chain 15 peptides. Score 0.496 Taking the results from Round 5 Chains 43, Residues 287, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 9203 restraints for refining 4074 atoms. 8098 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2683 (Rfree = 0.000) for 4074 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.2573 (Rfree = 0.000) for 4059 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2307 (Rfree = 0.000) for 4051 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2353 (Rfree = 0.000) for 4040 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2264 (Rfree = 0.000) for 4031 atoms. Found 5 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 4146 seeds are put forward Round 1: 292 peptides, 52 chains. Longest chain 12 peptides. Score 0.352 Round 2: 308 peptides, 42 chains. Longest chain 24 peptides. Score 0.466 Round 3: 328 peptides, 44 chains. Longest chain 18 peptides. Score 0.485 Round 4: 314 peptides, 41 chains. Longest chain 23 peptides. Score 0.484 Round 5: 314 peptides, 42 chains. Longest chain 21 peptides. Score 0.476 Taking the results from Round 3 Chains 46, Residues 284, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 9184 restraints for refining 4075 atoms. 8026 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2450 (Rfree = 0.000) for 4075 atoms. Found 12 (19 requested) and removed 17 (9 requested) atoms. Cycle 27: After refmac, R = 0.2266 (Rfree = 0.000) for 4050 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2210 (Rfree = 0.000) for 4037 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2224 (Rfree = 0.000) for 4030 atoms. Found 4 (19 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.2304 (Rfree = 0.000) for 4016 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 4111 seeds are put forward Round 1: 268 peptides, 47 chains. Longest chain 16 peptides. Score 0.347 Round 2: 293 peptides, 44 chains. Longest chain 26 peptides. Score 0.422 Round 3: 297 peptides, 46 chains. Longest chain 16 peptides. Score 0.413 Round 4: 305 peptides, 43 chains. Longest chain 27 peptides. Score 0.452 Round 5: 301 peptides, 44 chains. Longest chain 17 peptides. Score 0.437 Taking the results from Round 4 Chains 43, Residues 262, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 9437 restraints for refining 4074 atoms. 8432 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2471 (Rfree = 0.000) for 4074 atoms. Found 12 (19 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2422 (Rfree = 0.000) for 4046 atoms. Found 8 (19 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2302 (Rfree = 0.000) for 4026 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2251 (Rfree = 0.000) for 4018 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2265 (Rfree = 0.000) for 4010 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 2.93 Search for helices and strands: 0 residues in 0 chains, 4116 seeds are put forward Round 1: 226 peptides, 41 chains. Longest chain 12 peptides. Score 0.314 Round 2: 281 peptides, 45 chains. Longest chain 13 peptides. Score 0.391 Round 3: 291 peptides, 41 chains. Longest chain 19 peptides. Score 0.443 Round 4: 288 peptides, 41 chains. Longest chain 19 peptides. Score 0.438 Round 5: 298 peptides, 42 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 5 Chains 42, Residues 256, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 9216 restraints for refining 4073 atoms. 8154 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2443 (Rfree = 0.000) for 4073 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 37: After refmac, R = 0.2295 (Rfree = 0.000) for 4033 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. Cycle 38: After refmac, R = 0.2224 (Rfree = 0.000) for 4010 atoms. Found 14 (19 requested) and removed 17 (9 requested) atoms. Cycle 39: After refmac, R = 0.2203 (Rfree = 0.000) for 3997 atoms. Found 4 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.2195 (Rfree = 0.000) for 3986 atoms. Found 7 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 4110 seeds are put forward Round 1: 260 peptides, 50 chains. Longest chain 11 peptides. Score 0.304 Round 2: 287 peptides, 46 chains. Longest chain 12 peptides. Score 0.394 Round 3: 285 peptides, 45 chains. Longest chain 16 peptides. Score 0.398 Round 4: 284 peptides, 44 chains. Longest chain 16 peptides. Score 0.405 Round 5: 294 peptides, 43 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 43, Residues 251, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7253 reflections ( 95.17 % complete ) and 9450 restraints for refining 4075 atoms. 8459 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2660 (Rfree = 0.000) for 4075 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.2618 (Rfree = 0.000) for 4056 atoms. Found 18 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2597 (Rfree = 0.000) for 4047 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.2707 (Rfree = 0.000) for 4039 atoms. Found 13 (19 requested) and removed 12 (9 requested) atoms. Cycle 45: After refmac, R = 0.2826 (Rfree = 0.000) for 4038 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 2.98 Search for helices and strands: 0 residues in 0 chains, 4109 seeds are put forward Round 1: 235 peptides, 46 chains. Longest chain 9 peptides. Score 0.287 Round 2: 249 peptides, 39 chains. Longest chain 20 peptides. Score 0.380 Round 3: 273 peptides, 43 chains. Longest chain 16 peptides. Score 0.392 Round 4: 282 peptides, 40 chains. Longest chain 20 peptides. Score 0.435 Round 5: 282 peptides, 43 chains. Longest chain 19 peptides. Score 0.410 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 242, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1zy9-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7253 reflections ( 95.17 % complete ) and 9463 restraints for refining 4075 atoms. 8535 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2760 (Rfree = 0.000) for 4075 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2673 (Rfree = 0.000) for 4047 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2812 (Rfree = 0.000) for 4036 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2951 (Rfree = 0.000) for 4024 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:36:52 GMT 2018 Job finished. TimeTaking 68.92 Used memory is bytes: 2600480