null Sun 23 Dec 22:22:46 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 2ozg-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-2.0-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/2ozg-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-2.0-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 ============================================================ Sun 23 Dec 22:22:56 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/2ozg-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-2.0-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 371 and 0 Target number of residues in the AU: 371 Target solvent content: 0.5265 Checking the provided sequence file Detected sequence length: 396 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 396 Adjusted target solvent content: 0.49 Input MTZ file: 2ozg-2.0-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: 155 Cell parameters: 175.031 175.031 71.923 90.000 90.000 120.000 Input sequence file: 2ozg-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3168 target number of atoms Had to go as low as 0.50 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 1 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: 87.516 2.000 Wilson plot Bfac: 29.16 28431 reflections ( 99.87 % complete ) and 0 restraints for refining 3543 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Starting model: R = 0.3358 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2799 (Rfree = 0.000) for 3543 atoms. Found 102 (121 requested) and removed 68 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.18 2.21 Round 1: 258 peptides, 34 chains. Longest chain 23 peptides. Score 0.613 Round 2: 308 peptides, 30 chains. Longest chain 30 peptides. Score 0.763 Round 3: 336 peptides, 17 chains. Longest chain 76 peptides. Score 0.884 Round 4: 350 peptides, 18 chains. Longest chain 107 peptides. Score 0.891 Round 5: 358 peptides, 12 chains. Longest chain 99 peptides. Score 0.923 Taking the results from Round 5 Chains 12, Residues 346, Estimated correctness of the model 99.4 % 8 chains (319 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 125 A and 128 A Built loop between residues 206 A and 212 A Built loop between residues 221 A and 227 A Built loop between residues 241 A and 245 A Built loop between residues 342 A and 345 A 7 chains (363 residues) following loop building 3 chains (336 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3670 restraints for refining 3346 atoms. 865 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2822 (Rfree = 0.000) for 3346 atoms. Found 114 (114 requested) and removed 64 (57 requested) atoms. Cycle 2: After refmac, R = 0.2528 (Rfree = 0.000) for 3365 atoms. Found 83 (114 requested) and removed 58 (58 requested) atoms. Cycle 3: After refmac, R = 0.2395 (Rfree = 0.000) for 3376 atoms. Found 64 (111 requested) and removed 43 (58 requested) atoms. Cycle 4: After refmac, R = 0.2246 (Rfree = 0.000) for 3385 atoms. Found 79 (109 requested) and removed 32 (58 requested) atoms. Cycle 5: After refmac, R = 0.2160 (Rfree = 0.000) for 3422 atoms. Found 56 (110 requested) and removed 33 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.13 2.16 Round 1: 370 peptides, 8 chains. Longest chain 115 peptides. Score 0.944 Round 2: 372 peptides, 9 chains. Longest chain 152 peptides. Score 0.941 Round 3: 368 peptides, 10 chains. Longest chain 119 peptides. Score 0.936 Round 4: 375 peptides, 6 chains. Longest chain 128 peptides. Score 0.953 Round 5: 374 peptides, 7 chains. Longest chain 182 peptides. Score 0.949 Taking the results from Round 4 Chains 7, Residues 369, Estimated correctness of the model 99.7 % 6 chains (365 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 42 A Built loop between residues 168 A and 171 A Built loop between residues 206 A and 210 A Built loop between residues 222 A and 226 A Built loop between residues 346 A and 349 A 2 chains (387 residues) following loop building 1 chains (383 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3359 restraints for refining 3440 atoms. 252 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2299 (Rfree = 0.000) for 3440 atoms. Found 98 (108 requested) and removed 60 (58 requested) atoms. Cycle 7: After refmac, R = 0.2116 (Rfree = 0.000) for 3475 atoms. Found 73 (107 requested) and removed 58 (59 requested) atoms. Cycle 8: After refmac, R = 0.2000 (Rfree = 0.000) for 3479 atoms. Found 73 (105 requested) and removed 50 (59 requested) atoms. Cycle 9: After refmac, R = 0.1933 (Rfree = 0.000) for 3499 atoms. Found 78 (102 requested) and removed 47 (59 requested) atoms. Cycle 10: After refmac, R = 0.1869 (Rfree = 0.000) for 3528 atoms. Found 66 (101 requested) and removed 43 (60 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 2.17 Round 1: 381 peptides, 6 chains. Longest chain 169 peptides. Score 0.955 Round 2: 384 peptides, 4 chains. Longest chain 195 peptides. Score 0.962 Round 3: 380 peptides, 6 chains. Longest chain 171 peptides. Score 0.954 Round 4: 381 peptides, 7 chains. Longest chain 171 peptides. Score 0.952 Round 5: 382 peptides, 6 chains. Longest chain 189 peptides. Score 0.955 Taking the results from Round 2 Chains 4, Residues 380, Estimated correctness of the model 99.8 % 4 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 165 A Built loop between residues 181 A and 184 A Built loop between residues 377 A and 380 A 1 chains (386 residues) following loop building 1 chains (386 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3360 restraints for refining 3489 atoms. 240 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2072 (Rfree = 0.000) for 3489 atoms. Found 92 (98 requested) and removed 62 (59 requested) atoms. Cycle 12: After refmac, R = 0.1921 (Rfree = 0.000) for 3514 atoms. Found 87 (96 requested) and removed 60 (60 requested) atoms. Cycle 13: After refmac, R = 0.1858 (Rfree = 0.000) for 3535 atoms. Found 88 (94 requested) and removed 53 (60 requested) atoms. Cycle 14: After refmac, R = 0.1814 (Rfree = 0.000) for 3566 atoms. Found 83 (93 requested) and removed 62 (61 requested) atoms. Cycle 15: After refmac, R = 0.1787 (Rfree = 0.000) for 3584 atoms. Found 88 (90 requested) and removed 61 (61 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.13 2.16 Round 1: 384 peptides, 3 chains. Longest chain 230 peptides. Score 0.965 Round 2: 385 peptides, 3 chains. Longest chain 214 peptides. Score 0.965 Round 3: 377 peptides, 6 chains. Longest chain 152 peptides. Score 0.953 Round 4: 386 peptides, 2 chains. Longest chain 329 peptides. Score 0.968 Round 5: 380 peptides, 8 chains. Longest chain 171 peptides. Score 0.948 Taking the results from Round 4 Chains 3, Residues 384, Estimated correctness of the model 99.9 % 2 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A 2 chains (386 residues) following loop building 1 chains (382 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3392 restraints for refining 3478 atoms. 297 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2025 (Rfree = 0.000) for 3478 atoms. Found 86 (86 requested) and removed 61 (59 requested) atoms. Cycle 17: After refmac, R = 0.1897 (Rfree = 0.000) for 3500 atoms. Found 66 (83 requested) and removed 46 (59 requested) atoms. Cycle 18: After refmac, R = 0.1806 (Rfree = 0.000) for 3517 atoms. Found 82 (82 requested) and removed 39 (60 requested) atoms. Cycle 19: After refmac, R = 0.1778 (Rfree = 0.000) for 3557 atoms. Found 70 (82 requested) and removed 61 (60 requested) atoms. Cycle 20: After refmac, R = 0.1737 (Rfree = 0.000) for 3562 atoms. Found 81 (81 requested) and removed 49 (61 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 2.16 Round 1: 380 peptides, 4 chains. Longest chain 117 peptides. Score 0.961 Round 2: 383 peptides, 4 chains. Longest chain 170 peptides. Score 0.962 Round 3: 383 peptides, 4 chains. Longest chain 170 peptides. Score 0.962 Round 4: 377 peptides, 8 chains. Longest chain 151 peptides. Score 0.947 Round 5: 386 peptides, 3 chains. Longest chain 171 peptides. Score 0.966 Taking the results from Round 5 Chains 5, Residues 383, Estimated correctness of the model 99.9 % 3 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 223 A and 227 A 2 chains (387 residues) following loop building 2 chains (387 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3339 restraints for refining 3472 atoms. 216 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2000 (Rfree = 0.000) for 3472 atoms. Found 76 (76 requested) and removed 61 (59 requested) atoms. Cycle 22: After refmac, R = 0.1854 (Rfree = 0.000) for 3486 atoms. Found 74 (74 requested) and removed 27 (59 requested) atoms. Cycle 23: After refmac, R = 0.1776 (Rfree = 0.000) for 3532 atoms. Found 70 (75 requested) and removed 30 (60 requested) atoms. Cycle 24: After refmac, R = 0.1741 (Rfree = 0.000) for 3569 atoms. Found 64 (76 requested) and removed 45 (61 requested) atoms. Cycle 25: After refmac, R = 0.1713 (Rfree = 0.000) for 3587 atoms. Found 73 (73 requested) and removed 52 (61 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.12 2.15 Round 1: 377 peptides, 5 chains. Longest chain 198 peptides. Score 0.957 Round 2: 383 peptides, 4 chains. Longest chain 171 peptides. Score 0.962 Round 3: 382 peptides, 5 chains. Longest chain 152 peptides. Score 0.958 Round 4: 381 peptides, 6 chains. Longest chain 171 peptides. Score 0.955 Round 5: 382 peptides, 5 chains. Longest chain 199 peptides. Score 0.958 Taking the results from Round 2 Chains 5, Residues 379, Estimated correctness of the model 99.8 % 4 chains (378 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A Built loop between residues 195 A and 199 A Built loop between residues 224 A and 227 A 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3377 restraints for refining 3509 atoms. 266 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1984 (Rfree = 0.000) for 3509 atoms. Found 70 (70 requested) and removed 62 (60 requested) atoms. Cycle 27: After refmac, R = 0.1870 (Rfree = 0.000) for 3512 atoms. Found 67 (67 requested) and removed 36 (60 requested) atoms. Cycle 28: After refmac, R = 0.1793 (Rfree = 0.000) for 3542 atoms. Found 65 (65 requested) and removed 40 (60 requested) atoms. Cycle 29: After refmac, R = 0.1756 (Rfree = 0.000) for 3562 atoms. Found 63 (63 requested) and removed 43 (61 requested) atoms. Cycle 30: After refmac, R = 0.1739 (Rfree = 0.000) for 3580 atoms. Found 61 (61 requested) and removed 54 (61 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 2.16 Round 1: 384 peptides, 3 chains. Longest chain 213 peptides. Score 0.965 Round 2: 381 peptides, 6 chains. Longest chain 158 peptides. Score 0.955 Round 3: 384 peptides, 4 chains. Longest chain 190 peptides. Score 0.962 Round 4: 385 peptides, 4 chains. Longest chain 171 peptides. Score 0.962 Round 5: 378 peptides, 7 chains. Longest chain 133 peptides. Score 0.951 Taking the results from Round 1 Chains 3, Residues 381, Estimated correctness of the model 99.8 % 3 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 165 A Built loop between residues 181 A and 184 A 1 chains (385 residues) following loop building 1 chains (385 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3343 restraints for refining 3476 atoms. 235 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1958 (Rfree = 0.000) for 3476 atoms. Found 59 (59 requested) and removed 61 (59 requested) atoms. Cycle 32: After refmac, R = 0.1829 (Rfree = 0.000) for 3471 atoms. Found 59 (59 requested) and removed 16 (59 requested) atoms. Cycle 33: After refmac, R = 0.1755 (Rfree = 0.000) for 3513 atoms. Found 60 (60 requested) and removed 30 (60 requested) atoms. Cycle 34: After refmac, R = 0.1723 (Rfree = 0.000) for 3542 atoms. Found 60 (60 requested) and removed 43 (60 requested) atoms. Cycle 35: After refmac, R = 0.1705 (Rfree = 0.000) for 3558 atoms. Found 60 (60 requested) and removed 47 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.12 2.15 Round 1: 383 peptides, 3 chains. Longest chain 233 peptides. Score 0.965 Round 2: 380 peptides, 7 chains. Longest chain 195 peptides. Score 0.951 Round 3: 383 peptides, 5 chains. Longest chain 136 peptides. Score 0.959 Round 4: 381 peptides, 7 chains. Longest chain 140 peptides. Score 0.952 Round 5: 381 peptides, 7 chains. Longest chain 133 peptides. Score 0.952 Taking the results from Round 1 Chains 3, Residues 380, Estimated correctness of the model 99.8 % 3 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 38 A Built loop between residues 161 A and 164 A 1 chains (386 residues) following loop building 1 chains (386 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3325 restraints for refining 3474 atoms. 205 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1953 (Rfree = 0.000) for 3474 atoms. Found 59 (59 requested) and removed 59 (59 requested) atoms. Cycle 37: After refmac, R = 0.1818 (Rfree = 0.000) for 3471 atoms. Found 59 (59 requested) and removed 39 (59 requested) atoms. Cycle 38: After refmac, R = 0.1755 (Rfree = 0.000) for 3490 atoms. Found 59 (59 requested) and removed 32 (59 requested) atoms. Cycle 39: After refmac, R = 0.1705 (Rfree = 0.000) for 3517 atoms. Found 60 (60 requested) and removed 34 (60 requested) atoms. Cycle 40: After refmac, R = 0.1681 (Rfree = 0.000) for 3542 atoms. Found 60 (60 requested) and removed 43 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.11 2.14 Round 1: 383 peptides, 4 chains. Longest chain 227 peptides. Score 0.962 Round 2: 384 peptides, 4 chains. Longest chain 214 peptides. Score 0.962 Round 3: 383 peptides, 5 chains. Longest chain 216 peptides. Score 0.959 Round 4: 385 peptides, 3 chains. Longest chain 208 peptides. Score 0.965 Round 5: 376 peptides, 8 chains. Longest chain 195 peptides. Score 0.946 Taking the results from Round 4 Chains 4, Residues 382, Estimated correctness of the model 99.8 % 3 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 244 A and 247 A 2 chains (387 residues) following loop building 2 chains (387 residues) in sequence following loop building ------------------------------------------------------ 28431 reflections ( 99.87 % complete ) and 3307 restraints for refining 3473 atoms. 184 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1967 (Rfree = 0.000) for 3473 atoms. Found 59 (59 requested) and removed 60 (59 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 3471 atoms. Found 59 (59 requested) and removed 35 (59 requested) atoms. Cycle 43: After refmac, R = 0.1767 (Rfree = 0.000) for 3493 atoms. Found 58 (59 requested) and removed 43 (59 requested) atoms. Cycle 44: After refmac, R = 0.1743 (Rfree = 0.000) for 3506 atoms. Found 60 (60 requested) and removed 43 (60 requested) atoms. Cycle 45: After refmac, R = 0.1725 (Rfree = 0.000) for 3521 atoms. Found 60 (60 requested) and removed 43 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 2.16 Round 1: 380 peptides, 5 chains. Longest chain 170 peptides. Score 0.958 Round 2: 381 peptides, 6 chains. Longest chain 171 peptides. Score 0.955 Round 3: 380 peptides, 7 chains. Longest chain 133 peptides. Score 0.951 Round 4: 379 peptides, 8 chains. Longest chain 171 peptides. Score 0.948 Round 5: 381 peptides, 6 chains. Longest chain 152 peptides. Score 0.955 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 375, Estimated correctness of the model 99.8 % 5 chains (375 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 119 A and 122 A Built loop between residues 167 A and 170 A Built loop between residues 222 A and 227 A 1 chains (386 residues) following loop building 1 chains (386 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 28431 reflections ( 99.87 % complete ) and 3120 restraints for refining 3054 atoms. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2454 (Rfree = 0.000) for 3054 atoms. Found 52 (52 requested) and removed 0 (52 requested) atoms. Cycle 47: After refmac, R = 0.2257 (Rfree = 0.000) for 3054 atoms. Found 22 (53 requested) and removed 0 (53 requested) atoms. Cycle 48: After refmac, R = 0.2124 (Rfree = 0.000) for 3054 atoms. Found 17 (53 requested) and removed 1 (53 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 3054 atoms. Found 12 (53 requested) and removed 3 (53 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:36:42 GMT 2018 Job finished. TimeTaking 73.93 Used memory is bytes: 18835992