null Mon 24 Dec 07:35:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p8j-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:36:01 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/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.2-parrot-noncs/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 439 and 0 Target number of residues in the AU: 439 Target solvent content: 0.6324 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-3.2-parrot-noncs.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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.05 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: 72.625 3.201 Wilson plot Bfac: 67.57 11083 reflections ( 98.96 % complete ) and 0 restraints for refining 3693 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Starting model: R = 0.3355 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2632 (Rfree = 0.000) for 3693 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3768 seeds are put forward NCS extension: 0 residues added, 3768 seeds are put forward Round 1: 283 peptides, 39 chains. Longest chain 22 peptides. Score 0.508 Round 2: 320 peptides, 36 chains. Longest chain 29 peptides. Score 0.610 Round 3: 335 peptides, 30 chains. Longest chain 29 peptides. Score 0.683 Round 4: 338 peptides, 33 chains. Longest chain 39 peptides. Score 0.665 Round 5: 318 peptides, 29 chains. Longest chain 41 peptides. Score 0.663 Taking the results from Round 3 Chains 34, Residues 305, Estimated correctness of the model 61.5 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5593 restraints for refining 3101 atoms. 4139 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2683 (Rfree = 0.000) for 3101 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 2: After refmac, R = 0.2561 (Rfree = 0.000) for 3071 atoms. Found 21 (27 requested) and removed 14 (13 requested) atoms. Cycle 3: After refmac, R = 0.2484 (Rfree = 0.000) for 3065 atoms. Found 9 (27 requested) and removed 14 (13 requested) atoms. Cycle 4: After refmac, R = 0.2413 (Rfree = 0.000) for 3053 atoms. Found 1 (27 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.2357 (Rfree = 0.000) for 3039 atoms. Found 4 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.62 Search for helices and strands: 0 residues in 0 chains, 3129 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3147 seeds are put forward Round 1: 335 peptides, 29 chains. Longest chain 34 peptides. Score 0.691 Round 2: 338 peptides, 29 chains. Longest chain 34 peptides. Score 0.695 Round 3: 324 peptides, 28 chains. Longest chain 35 peptides. Score 0.681 Round 4: 331 peptides, 28 chains. Longest chain 23 peptides. Score 0.692 Round 5: 333 peptides, 30 chains. Longest chain 45 peptides. Score 0.680 Taking the results from Round 2 Chains 33, Residues 309, Estimated correctness of the model 64.1 % 5 chains (106 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5088 restraints for refining 3076 atoms. 3425 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2693 (Rfree = 0.000) for 3076 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 7: After refmac, R = 0.2623 (Rfree = 0.000) for 3060 atoms. Found 25 (27 requested) and removed 15 (13 requested) atoms. Cycle 8: After refmac, R = 0.2638 (Rfree = 0.000) for 3057 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2557 (Rfree = 0.000) for 3049 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 10: After refmac, R = 0.2282 (Rfree = 0.000) for 3044 atoms. Found 12 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 3131 seeds are put forward NCS extension: 16 residues added (11 deleted due to clashes), 3147 seeds are put forward Round 1: 335 peptides, 24 chains. Longest chain 50 peptides. Score 0.727 Round 2: 326 peptides, 28 chains. Longest chain 33 peptides. Score 0.684 Round 3: 335 peptides, 27 chains. Longest chain 47 peptides. Score 0.705 Round 4: 335 peptides, 23 chains. Longest chain 79 peptides. Score 0.733 Round 5: 345 peptides, 22 chains. Longest chain 73 peptides. Score 0.753 Taking the results from Round 5 Chains 25, Residues 323, Estimated correctness of the model 75.6 % 5 chains (131 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 106 A 24 chains (326 residues) following loop building 4 chains (134 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4832 restraints for refining 3088 atoms. 2976 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2695 (Rfree = 0.000) for 3088 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 12: After refmac, R = 0.2442 (Rfree = 0.000) for 3074 atoms. Found 13 (26 requested) and removed 15 (13 requested) atoms. Cycle 13: After refmac, R = 0.2548 (Rfree = 0.000) for 3060 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.2503 (Rfree = 0.000) for 3060 atoms. Found 20 (25 requested) and removed 16 (13 requested) atoms. Cycle 15: After refmac, R = 0.2279 (Rfree = 0.000) for 3060 atoms. Found 11 (25 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 3128 seeds are put forward NCS extension: 47 residues added (7 deleted due to clashes), 3175 seeds are put forward Round 1: 333 peptides, 28 chains. Longest chain 33 peptides. Score 0.695 Round 2: 329 peptides, 25 chains. Longest chain 46 peptides. Score 0.711 Round 3: 327 peptides, 31 chains. Longest chain 47 peptides. Score 0.663 Round 4: 330 peptides, 25 chains. Longest chain 43 peptides. Score 0.712 Round 5: 326 peptides, 27 chains. Longest chain 36 peptides. Score 0.692 Taking the results from Round 4 Chains 28, Residues 305, Estimated correctness of the model 67.7 % 5 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 121 A Built loop between residues 162 B and 168 B 25 chains (312 residues) following loop building 3 chains (105 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4997 restraints for refining 3053 atoms. 3357 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2676 (Rfree = 0.000) for 3053 atoms. Found 24 (24 requested) and removed 29 (13 requested) atoms. Cycle 17: After refmac, R = 0.2532 (Rfree = 0.000) for 3027 atoms. Found 21 (24 requested) and removed 23 (13 requested) atoms. Cycle 18: After refmac, R = 0.2757 (Rfree = 0.000) for 3016 atoms. Found 23 (23 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2763 (Rfree = 0.000) for 3013 atoms. Found 23 (23 requested) and removed 24 (13 requested) atoms. Cycle 20: After refmac, R = 0.2416 (Rfree = 0.000) for 3005 atoms. Found 12 (22 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.57 Search for helices and strands: 0 residues in 0 chains, 3092 seeds are put forward NCS extension: 45 residues added (12 deleted due to clashes), 3137 seeds are put forward Round 1: 319 peptides, 33 chains. Longest chain 23 peptides. Score 0.633 Round 2: 314 peptides, 28 chains. Longest chain 42 peptides. Score 0.665 Round 3: 320 peptides, 28 chains. Longest chain 30 peptides. Score 0.675 Round 4: 328 peptides, 28 chains. Longest chain 42 peptides. Score 0.687 Round 5: 323 peptides, 29 chains. Longest chain 25 peptides. Score 0.672 Taking the results from Round 4 Chains 30, Residues 300, Estimated correctness of the model 62.3 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5809 restraints for refining 3052 atoms. 4395 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2619 (Rfree = 0.000) for 3052 atoms. Found 22 (22 requested) and removed 16 (13 requested) atoms. Cycle 22: After refmac, R = 0.2497 (Rfree = 0.000) for 3047 atoms. Found 15 (22 requested) and removed 13 (13 requested) atoms. Cycle 23: After refmac, R = 0.2359 (Rfree = 0.000) for 3044 atoms. Found 13 (22 requested) and removed 13 (13 requested) atoms. Cycle 24: After refmac, R = 0.2278 (Rfree = 0.000) for 3041 atoms. Found 5 (22 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2204 (Rfree = 0.000) for 3030 atoms. Found 5 (22 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3109 seeds are put forward NCS extension: 25 residues added (14 deleted due to clashes), 3134 seeds are put forward Round 1: 290 peptides, 34 chains. Longest chain 22 peptides. Score 0.570 Round 2: 318 peptides, 27 chains. Longest chain 25 peptides. Score 0.679 Round 3: 311 peptides, 27 chains. Longest chain 39 peptides. Score 0.668 Round 4: 325 peptides, 27 chains. Longest chain 42 peptides. Score 0.690 Round 5: 308 peptides, 30 chains. Longest chain 30 peptides. Score 0.638 Taking the results from Round 4 Chains 27, Residues 298, Estimated correctness of the model 63.0 % 4 chains (84 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5474 restraints for refining 3053 atoms. 3951 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2613 (Rfree = 0.000) for 3053 atoms. Found 22 (22 requested) and removed 20 (13 requested) atoms. Cycle 27: After refmac, R = 0.2443 (Rfree = 0.000) for 3049 atoms. Found 22 (22 requested) and removed 19 (13 requested) atoms. Cycle 28: After refmac, R = 0.2417 (Rfree = 0.000) for 3048 atoms. Found 18 (22 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.2337 (Rfree = 0.000) for 3047 atoms. Found 14 (22 requested) and removed 14 (13 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 3043 atoms. Found 9 (22 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 3145 seeds are put forward Round 1: 309 peptides, 34 chains. Longest chain 22 peptides. Score 0.606 Round 2: 317 peptides, 28 chains. Longest chain 39 peptides. Score 0.670 Round 3: 315 peptides, 29 chains. Longest chain 39 peptides. Score 0.658 Round 4: 294 peptides, 30 chains. Longest chain 26 peptides. Score 0.613 Round 5: 332 peptides, 30 chains. Longest chain 32 peptides. Score 0.678 Taking the results from Round 5 Chains 32, Residues 302, Estimated correctness of the model 60.3 % 4 chains (75 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5565 restraints for refining 3052 atoms. 4058 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2581 (Rfree = 0.000) for 3052 atoms. Found 22 (22 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.2371 (Rfree = 0.000) for 3050 atoms. Found 12 (22 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.2294 (Rfree = 0.000) for 3041 atoms. Found 11 (22 requested) and removed 15 (13 requested) atoms. Cycle 34: After refmac, R = 0.2233 (Rfree = 0.000) for 3037 atoms. Found 7 (22 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2163 (Rfree = 0.000) for 3030 atoms. Found 4 (22 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3102 seeds are put forward NCS extension: 37 residues added (7 deleted due to clashes), 3139 seeds are put forward Round 1: 293 peptides, 32 chains. Longest chain 22 peptides. Score 0.594 Round 2: 313 peptides, 26 chains. Longest chain 42 peptides. Score 0.679 Round 3: 317 peptides, 22 chains. Longest chain 48 peptides. Score 0.715 Round 4: 315 peptides, 28 chains. Longest chain 31 peptides. Score 0.666 Round 5: 320 peptides, 26 chains. Longest chain 39 peptides. Score 0.690 Taking the results from Round 3 Chains 25, Residues 295, Estimated correctness of the model 68.3 % 3 chains (93 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 183 A and 193 A 23 chains (303 residues) following loop building 2 chains (102 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5292 restraints for refining 3073 atoms. 3655 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2548 (Rfree = 0.000) for 3073 atoms. Found 22 (22 requested) and removed 24 (13 requested) atoms. Cycle 37: After refmac, R = 0.2497 (Rfree = 0.000) for 3064 atoms. Found 21 (21 requested) and removed 17 (13 requested) atoms. Cycle 38: After refmac, R = 0.2544 (Rfree = 0.000) for 3062 atoms. Found 21 (21 requested) and removed 16 (13 requested) atoms. Cycle 39: After refmac, R = 0.2522 (Rfree = 0.000) for 3064 atoms. Found 20 (20 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.2548 (Rfree = 0.000) for 3066 atoms. Found 19 (19 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3158 seeds are put forward NCS extension: 42 residues added (9 deleted due to clashes), 3200 seeds are put forward Round 1: 305 peptides, 24 chains. Longest chain 38 peptides. Score 0.682 Round 2: 305 peptides, 27 chains. Longest chain 32 peptides. Score 0.658 Round 3: 305 peptides, 30 chains. Longest chain 39 peptides. Score 0.633 Round 4: 307 peptides, 30 chains. Longest chain 27 peptides. Score 0.637 Round 5: 310 peptides, 27 chains. Longest chain 39 peptides. Score 0.666 Taking the results from Round 1 Chains 25, Residues 281, Estimated correctness of the model 61.2 % 3 chains (91 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5506 restraints for refining 3053 atoms. 4011 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2619 (Rfree = 0.000) for 3053 atoms. Found 19 (19 requested) and removed 22 (13 requested) atoms. Cycle 42: After refmac, R = 0.2636 (Rfree = 0.000) for 3040 atoms. Found 19 (19 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.2568 (Rfree = 0.000) for 3037 atoms. Found 19 (19 requested) and removed 19 (13 requested) atoms. Cycle 44: After refmac, R = 0.2557 (Rfree = 0.000) for 3033 atoms. Found 19 (19 requested) and removed 17 (13 requested) atoms. Cycle 45: After refmac, R = 0.2490 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward NCS extension: 27 residues added (23 deleted due to clashes), 3121 seeds are put forward Round 1: 301 peptides, 28 chains. Longest chain 31 peptides. Score 0.643 Round 2: 318 peptides, 24 chains. Longest chain 39 peptides. Score 0.702 Round 3: 318 peptides, 26 chains. Longest chain 39 peptides. Score 0.687 Round 4: 328 peptides, 25 chains. Longest chain 39 peptides. Score 0.709 Round 5: 315 peptides, 32 chains. Longest chain 44 peptides. Score 0.634 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 303, Estimated correctness of the model 67.0 % 5 chains (109 residues) have been docked in sequence Sequence coverage is 35 % Consider running further cycles of model building using 2p8j-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 162 A and 165 A Built loop between residues 185 A and 193 A 25 chains (310 residues) following loop building 3 chains (118 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11083 reflections ( 98.96 % complete ) and 5128 restraints for refining 3066 atoms. 3401 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2617 (Rfree = 0.000) for 3066 atoms. Found 0 (19 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2643 (Rfree = 0.000) for 3044 atoms. Found 0 (18 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2660 (Rfree = 0.000) for 3028 atoms. Found 0 (18 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2603 (Rfree = 0.000) for 3010 atoms. Found 0 (17 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:22:32 GMT 2018 Job finished. TimeTaking 46.61 Used memory is bytes: 9176952